NOISE REDUCTION FOR DATA STORAGE IN DNA

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to and the benefit of U.S. Provisional Patent Application No. 63/417,809, filed October 20, 2022, and entitled “METHODS FOR NOISE REDUCTION”, the contents of which are incorporated herein by reference in their entirety.

BACKGROUND

[0002] Nucleic acid digital data storage is a stable approach for encoding and storing information for long periods of time, with data stored at higher densities than magnetic tape or hard drive storage systems. Additionally, digital data stored in nucleic acid molecules that are stored in cold and dry conditions can be retrieved as long as 60,000 years later or longer.

[0003] To access digital data stored in nucleic acid molecules, the nucleic acid molecules may be sequenced. As such, nucleic acid digital data storage may be an ideal method for storing data that is not frequently accessed but may have a high volume of information to be stored or archived for long periods of time.

[0004] Current methods rely on encoding the digital information (e.g., binary code) into base-by- base nucleic acids sequences, such that the base to base relationship in the sequence directly translates into the digital information (e.g., binary code). Sequencing of digital data stored in base-by-base sequences that can be read into bit-streams or bytes of digitally encoded information can be error prone and costly to encode since the cost of de novo base-by-base nucleic acid synthesis can be expensive. Opportunities for new methods of performing nucleic acid digital data storage may provide approaches for encoding and retrieving data that are less costly and easier to commercially implement.

SUMMARY

[0005] The systems, assemblies, and methods of the present disclosure generally relate to creation of DNA molecules that store digital information. For example, component nucleic acid molecules (e.g., components) are selected and individually dispensed onto a substrate material such as a webbing. The components are printed or dispensed at the same location (e.g., coordinate) on the substrate so as to be co-located. The components are configured to selfassemble, or otherwise sort themselves in a predetermined order, to form identifier nucleic acid molecules (e.g., identifiers). Each identifier corresponds to a particular symbol (e.g., bit or series of bits), or that symbol’s position (e.g., rank or address), in a string of symbols (e.g., a bitstream). To assemble the components, the system may print or dispense a reaction mix onto the same location, which causes the components to align themselves to form identifiers. The system may alternatively or additionally provide a condition necessary to physically link the components, such as a particular temperature that causes the components to align. Once formed, multiple identifiers may be combined into a pool of identifiers, where the pool is representative of at least a portion of the entire string of symbols.

[0006] Described in this specification are technologies for writing information into nucleic acid molecules (e.g., DNA), storing, and/or reading information encoded in nucleic acid molecules. Methods and systems of the present disclosure can be used to encode computer data or information in a plurality of identifiers, each of which can represent one or more bits of the original information. The technologies include methods to mitigate recombination generated by PCR, e.g., by the targeted removal of incompletely assembled products and/or blocking extension from non-primer DNA molecules. These technologies aim to improve the fidelity of identifier libraries during amplification steps by reducing chimeric identifier formation. Ultimately, reducing chimeric identifiers in the root library can improve decodability of identifier libraries. [0007] In an aspect, the present disclosure provides a method for writing information into a nucleic acid molecule with reduced noise. The method includes: determining a string of symbols to represent said information and generating a plurality of oligonucleotides including a plurality of identifiers. An individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols. Generating the plurality of oligonucleotides includes: (a) constructing a plurality of components, wherein each individual component of said plurality of oligonucleotides is a nucleic acid molecule having a nucleic acid sequence, a 3’-end, and a 5’- end; (b) adding, to a reaction volume including the plurality of components, a first volume including a template-independent polymerase and an amount of dideoxynucleotides (ddNTPs); (c) incubating the reaction volume to attach a ddNTP to the 3 ’-ends of at least a portion of the components; (d) adding, to the reaction volume, a reagent to chemically link together two or more components of said plurality of components, thereby generating the plurality of identifiers and a plurality of fragments; and (e) adding, to the reaction volume, PCR primers and subsequently performing PCR amplification, wherein PCR amplification of any oligonucleotide including a ddNTP is inhibited.

[0008] In and aspect, the present disclosure provides a method for writing information into a nucleic acid molecule. The method includes determining a string of symbols to represent said information and generating a plurality of oligonucleotides including a plurality of identifiers. An individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols. Generating the plurality of oligonucleotides includes: (a) constructing a plurality of components, wherein each individual component of said plurality of oligonucleotides is a nucleic acid molecule having a nucleic acid sequence, a 3 ’-end, and a 5 ’-end; (b) adding, to a reaction volume including the plurality of components, a first volume including a polymerase and an amount of acyclonucleotides; (c) incubating the reaction volume to attach an acyclonucleotide to the 3 ’-ends of at least a portion of the components; (d) adding, to the reaction volume, a reagent to chemically link together two or more components of said plurality of components, thereby generating the plurality of identifiers and a plurality of fragments; and (e) adding, to the reaction volume, PCR primers and subsequently perform PCR amplification, wherein PCR amplification of any oligonucleotide including an acyclonucleotides is inhibited.

[0009] In and aspect, the present disclosure provides a method for writing information into a nucleic acid molecule. The method includes determining a string of symbols to represent said information and generating a plurality of oligonucleotides including a plurality of identifiers. An individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols. Generating the plurality of oligonucleotides includes: (a) constructing a plurality of components, wherein each individual component of said plurality of oligonucleotides is a nucleic acid molecule having a nucleic acid sequence, a 3 ’-end, and a 5 ’-end; (b) adding, to the reaction volume, a reagent to chemically link together two or more components of said plurality of components, thereby generating the plurality of identifiers and a plurality of fragments; (c) adding, to a reaction volume including the plurality of components, a first volume including a polymerase and a plurality of 3’-DNA flaps; (d) incubating the reaction volume to attach a 3’-DNA flap to the 3’-ends of at least a portion of the components and fragments; and (e) adding, to the reaction volume, PCR primers and subsequently performing PCR amplification, wherein PCR amplification of any oligonucleotide including a 3’-DNA flap is inhibited. [0010] In and aspect, the present disclosure provides a method for writing information into a nucleic acid molecule. The method includes: (a) determining a string of symbols to represent said information; (b) constructing a plurality of components, wherein each individual component of said plurality of components is a nucleic acid molecule having a nucleic acid sequence, a 3 ’-end, and a 5 ’-end; (c) chemically linking together two or more components of said plurality of components thereby generating a plurality of identifiers, wherein each identifier of said plurality of identifiers includes two or more components, each identifier having a first end and a second end, each component disposed at the first end of the identifier being a first edge component, and each component disposed at the second end of the identifier being a second edge component; and (d) chemically modifying terminal ends of each of the first edge component, the second edge component, or both, such that first edge component and/or the second edge components are protected from exonuclease activity, wherein an individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols. INCORPORATION BY REFERENCE

[0011] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.

BRIEF DESCRIPTION OF THE DRAWINGS

[0012] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative implementations, in which the principles of the invention are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein).

[0013] FIG. 1 illustrates an example system for storing digital information in DNA by assembling DNA identifiers from components in rapid and high throughput manner using inkjet printing. The system and its different embodiments will henceforth be referred to as the "Printer- Finisher System" or PFS.

[0014] FIG. 2 shows an example of printer subsystem in more detail. The printheads are designed to overprint different components to the same coordinates on the web.

[0015] FIGs. 3A-3D depict an example of a printhead in the printer.

[0016] FIG. 4 depicts potential arrangements of the printheads within the printer.

[0017] FIG. 5 demonstrates an example set up for the spot imager in the printer subsystem.

[0018] FIG. 6 shows an example of the finisher subsystem in more detail. In addition to a part that dispenses reaction mix onto each coordinate of a substrate, the finisher may also comprise a part that dispenses a reaction inhibitor onto each coordinate of a substrate prior to consolidation. [0019] FIG. 7 shows an example of a loop of rollers for passing the web through the finisher during the incubation phase.

[0020] FIG. 8 illustrates the effect of reaction mix glycerol composition and finisher humidity on the anticipated equilibrium volume during incubation.

[0021] FIG. 9 illustrates an example pooling system that consolidates all reactions from the web into one container.

[0022] FIG. 10 depicts a schematic of an embodiment of the data transfer pipeline through the PFS.

[0023] FIG. 11 illustrates an embodiment of the PFS that comprises four modules: a chassis module, a print engine module, an incubator module, and a pooling module.

[0024] FIG. 12 illustrates an embodiment of the PFS that pools reaction droplets into an emulsion.

[0025] FIG. 13 illustrates an embodiment of the PFS where reaction droplets are coated with oil (or another non-miscible liquid) after being printed onto the webbing.

[0026] FIG. 14 illustrates an embodiment of the PFS where reaction droplets contain beads that bind the printed DNA components.

[0027] FIG. 15 illustrates an example of how DNA components bound onto beads may be processed into identifiers using an emulsion.

[0028] FIG. 16 is a diagram illustrating the principle of operation of an implementation of the noise reduction technologies described in this specification.

[0029] FIG. 17 is an image of an agarose gel following electrophoresis with products of amplification of a 360bp block using two types of primers. Lane 3: unmodified primers. Lane 6: same set of primers as lane 3 and containing 3’ ddNTP.

[0030] FIGS. 18A-18Care graphs representing Agilent® Tapestation® (automated gel electrophoresis) results showing sample intensities vs. fragment length of products of: (A) 9- layer ligation, (B) 9-layer ligation treated with dNTPs only, (C) 9-layer ligation treated with ddNTPs and dNTPs.

[0031] FIG. 19 is a diagram illustrating a comparison of 5’ and 3’ overhangs.

[0032] FIGS. 20A-20B are flow diagrams illustrating example post-processing workflows with noise reduction steps for excised (FIG. 20A) and pooler (FIG. 20B) runs.

[0033] FIG. 21 is a diagram illustrating the principle of overhang-specific oligonucleotides containing 3’ flap as a mechanism of preventing amplification from unligated product.

[0034] FIG. 22 is a diagram illustrating the principle of an example nuclease-based noise reduction process.

[0035] FIG. 23 is a diagram illustrating the principle of an example hairpin loop-based FLIs protection and noise reduction process.

[0036] FIG. 24 is a diagram illustrating an example of a Protelomerase recognition site and resulting edge protection.

[0037] FIG. 25 is a diagram illustrating the principle of an example protelomerase based FLI protection and noise reduction process.

[0038] FIG. 26 is a diagram illustrating RP and SP configurations caused by phosphorothionate bonds. Image from NEB website.

[0039] FIG. 27 is a diagram illustrating inverted dT linkage.

[0040] FIG. 28 is a diagram illustrating sugar modifications that can protect FLIs from nucleases.

DETAILED DESCRIPTION

Definitions

[0041] The term “component,” as used herein, generally refers to a nucleic acid sequence. A component may be a distinct nucleic acid sequence. A component may be concatenated or assembled with one or more other components to generate other nucleic acid sequence or molecules. [0042] The term “layer,” as used herein, generally refers to group or pool of components. Each layer may comprise a set of distinct components such that the components in one layer are different from the components in another layer. Components from one or more layers may be assembled to generate one or more identifiers.

[0043] The term “identifier,” as used herein, generally refers to a nucleic acid molecule or a nucleic acid sequence that represents the position and value of a bit-string within a larger bitstring. More generally, an identifier may refer to any object that represents or corresponds to a symbol in a string of symbols. In some implementations, identifiers may comprise one or multiple concatenated components.

[0044] The term “identifier library,” as used herein generally refers to a collection of identifiers corresponding to the symbols in a symbol string representing digital information. In some implementations, the absence of a given identifier in the identifier library may indicate a symbol value at a particular position. One or more identifier libraries may be combined in a pool, group, or set of identifiers. Each identifier library may include a unique barcode that identifies the identifier library.

[0045] The term “nucleic acid,” as used herein, general refers to deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or a variant thereof. A nucleic acid may include one or more subunits selected from adenosine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), or variants thereof. A nucleotide can include A, C, G, T, or U, or variants thereof. A nucleotide can include any subunit that can be incorporated into a growing nucleic acid strand. Such subunit can be A, C, G, T, or U, or any other subunit that may be specific to one of more complementary A, C, G, T, or U, or complementary to a purine (i.e., A or G, or variant thereof) or pyrimidine (i.e., C, T, or U, or variant thereof). In some examples, a nucleic acid may be single-stranded or double stranded, in some cases, a nucleic acid is circular.

[0046] The terms “nucleic acid molecule” or “nucleic acid sequence,” as used herein, generally refer to a polymeric form of nucleotides, or polynucleotide, that may have various lengths, either deoxyribonucleotides (DNA) or ribonucleotides (RNA), or analogs thereof. The term "nucleic acid sequence" may refer to the alphabetical representation of a polynucleotide; alternatively, the term may be applied to the physical polynucleotide itself. This alphabetical representation can be input into databases in a computer having a central processing unit and used for mapping nucleic acid sequences or nucleic acid molecules to symbols, or bits, encoding digital information. Nucleic acid sequences or oligonucleotides may include one or more non-standard nucleotide(s), nucleotide analog(s) and/or modified nucleotides.

[0047] An "oligonucleotide", as used herein, generally refers to a single-stranded nucleic acid sequence, and is typically composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G), and thymine (T) or uracil (U) when the polynucleotide is RNA.

[0048] Examples of modified nucleotides include, but are not limited to diaminopurine, 5- fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4- acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5- carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6- isopentenyladenine, 1-methylguanine, 1 -methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3 -methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5- methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'- methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-D46-isopentenyladenine, uracil-5- oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl)uracil, (acp3)w, 2,6- diaminopurine and the like. Nucleic acid molecules may also be modified at the base moiety (e.g., at one or more atoms that typically are available to form a hydrogen bond with a complementary nucleotide and/or at one or more atoms that are not typically capable of forming a hydrogen bond with a complementary nucleotide), sugar moiety or phosphate backbone.

Nucleic acid molecules may also contain amine-modified groups, such as aminoallyl-dUTP (aa- dUTP) and aminohexhylacrylamide-dCTP (aha-dCTP) to allow covalent attachment of amine reactive moieties, such as N-hydroxy succinimide esters (NHS).

[0049] The term “primer,” as used herein, generally refers to a strand of nucleic acid that serves as a starting point for nucleic acid synthesis, such as polymerase chain reaction (PCR). In an example, during replication of a DNA sample, an enzyme that catalyzes replication starts replication at the 3 '-end of a primer attached to the DNA sample and copies the opposite strand. [0050] The term "polymerase" or “polymerase enzyme,” as used herein, generally refers to any enzyme capable of catalyzing a polymerase reaction. Examples of polymerases include, without limitation, a nucleic acid polymerase. The polymerase can be naturally occurring or synthesized. An example polymerase is a 029 polymerase or derivative thereof. In some cases, a transcriptase or a ligase is used (i.e., enzymes which catalyze the formation of a bond) in conjunction with polymerases or as an alternative to polymerases to construct new nucleic acid sequences.

Examples of polymerases include a DNA polymerase, a RNA polymerase, a thermostable polymerase, a wild-type polymerase, a modified polymerase, E. coli DNA polymerase I, T7 DNA polymerase, bacteriophage T4 DNA polymerase 029 (phi29) DNA polymerase, Taq polymerase, Tth polymerase, Tli polymerase, Pfu polymerase Pwo polymerase, VENT polymerase, DEEPVENT polymerase, Ex-Taq polymerase, LA-Taw polymerase, Sso polymerase Poc polymerase, Pab polymerase, Mth polymerase ES4 polymerase, Tru polymerase, Tac polymerase, Tne polymerase, Tma polymerase, Tea polymerase, Tih polymerase, Tfi polymerase, Platinum Taq polymerases, Tbr polymerase, Tfl polymerase, Pfutubo polymerase, Pyrobest polymerase, KOD polymerase, Bst polymerase, Sac polymerase, Klenow fragment polymerase with 3’ to 5’ exonuclease activity, and variants, modified products and derivatives thereof.

[0051] Digital information, such as computer data, in the form of binary code can comprise a sequence or string of symbols. A binary code may encode or represent text or computer processor instructions using, for example, a binary number system having two binary symbols, typically 0 and 1, referred to as bits. Digital information may be represented in the form of non-binary code which can comprise a sequence of non-binary symbols. Each encoded symbol can be re-assigned to a unique bit string (or "byte"), and the unique bit string or byte can be arranged into strings of bytes or byte streams. A bit value for a given bit can be one of two symbols (e.g., 0 or 1). A byte, which can comprise a string of N bits, can have a total of 2N unique byte-values. For example, a byte comprising 8 bits can produce a total of 28 or 256 possible unique byte-values, and each of the 256 bytes can correspond to one of 256 possible distinct symbols, letters, or instructions which can be encoded with the bytes. Raw data (e.g., text files and computer instructions) can be represented as strings of bytes or byte streams. Zip files, or compressed data files comprising raw data can also be stored in byte streams, these files can be stored as byte streams in a compressed form, and then decompressed into raw data before being read by the computer.

Overview

[0052] Previous methods for encoding digital information into nucleic acids using inkjet printer systems have relied on base-by-base synthesis of the nucleic acids, which can be both costly and time consuming. For instance, inkjet printer based technologies have been previously used for oligonucleotide synthesis on a microreactor chip. However, these technologies utilize base-by- base synthesis which requires utilization of a four-step (deprotection, coupling, capping, and oxidation) solid-phase phosphoramidite cycle reaction for the addition of a single oligonucleotide during each round of synthesis. New methods described herein can encode digital information using combinatorial arrangements of components, wherein each component (e.g. nucleic acid sequence) is dispensed (e.g. printed) onto a substrate, and a reaction mixture and/or a condition is provided such that each of the components are physically linked in a single reaction.

[0053] Information can be stored in nucleic acid sequences. In some aspects of the present disclosure, provided herein are methods to encode digital information into identifiers which are built from one or more components. Each component can comprise a nucleic acid sequence. A print-based system, known as the Printer-Finisher System (or PFS), may be used to collocate and assemble components for construction of identifiers. A PFS may comprise two sub-systems, a printer and a finisher. A PFS may comprise one system, a printer which dispenses both the components and reaction mix onto a substrate. In some implementations, the two subsystems may be attached and dependent on each other for individual function. In other implementations, the two subsystems may be disjoint and capable of functioning independently.

Methods for encoding and writing information to nucleic acid sequence(s)

[0054] In an aspect, the present disclosure provides methods for encoding information into nucleic acid sequences. A method for encoding information into nucleic acid sequences may comprise (a) translating the information into a string of symbols, (b) mapping the string of symbols to a plurality of identifiers, and (c) constructing an identifier library comprising at least a subset of the plurality of identifiers. An individual identifier of the plurality of identifiers may comprise one or more components. An individual component of the one or more components may comprise a nucleic acid sequence. Each symbol at each position in the string of symbols may correspond to a distinct identifier. The individual identifier may correspond to an individual symbol at an individual position in the string of symbols. Moreover, one symbol at each position in the string of symbols may correspond to the absence of an identifier. For example, in a string of binary symbols (e.g., bits) of '0's and T's, each occurrence of 'O' may correspond to the absence of an identifier.

[0055] In another aspect, the present disclosure provides methods for nucleic acid-based computer data storage. A method for nucleic acid-based computer data storage may comprise (a) receiving computer data, (b) synthesizing nucleic acid molecules comprising nucleic acid sequences encoding the computer data, and (c) storing the nucleic acid molecules having the nucleic acid sequences. The computer data may be encoded in at least a subset of nucleic acid molecules synthesized and not in a sequence of each of the nucleic acid molecules.

[0056] In another aspect, the present disclosure provides methods for writing and storing information in nucleic acid sequences. The method may comprise, (a) receiving or encoding a virtual identifier library that represents information, (b) physically constructing the identifier library, and (c) storing one or more physical copies of the identifier library in one or more separate locations. An individual identifier of the identifier library may comprise one or more components. An individual component of the one or more components may comprise a nucleic acid sequence.

[0057] In another aspect, the present disclosure provides methods for nucleic acid-based computer data storage. A method for nucleic acid-based computer data storage may comprise (a) receiving computer data, (b) synthesizing a nucleic acid molecule comprising at least one nucleic acid sequence encoding the computer data, and (c) storing the nucleic acid molecule comprising the at least one nucleic acid sequence. Synthesizing the nucleic acid molecule may be in the absence of base-by-base nucleic acid synthesis.

[0058] In another aspect, the present disclosure provides methods for writing and storing information in nucleic acid sequences. A method for writing and storing information in nucleic acid sequences may comprise, (a) receiving or encoding a virtual identifier library that represents information, (b) physically constructing the identifier library, and (c) storing one or more physical copies of the identifier library in one or more separate locations. An individual identifier of the identifier library may comprise one or more components. An individual component of the one or more components may comprise a nucleic acid sequence.

Methods for reading information stored in nucleic acid sequences

[0059] In another aspect, the present disclosure provides methods for reading information encoded in nucleic acid sequences. A method for reading information encoded in nucleic acid sequences may comprise (a) providing an identifier library, (b) identifying the identifiers present in the identifier library, (c) generating a string of symbols from the identifiers present in the identifier library, and (d) compiling information from the string of symbols. An identifier library may comprise a subset of a plurality of identifiers from a combinatorial space. Each individual identifier of the subset of identifiers may correspond to an individual symbol in a string of symbols. An identifier may comprise one or more components. A component may comprise a nucleic acid sequence.

[0060] Information may be written into one or more identifier libraries as described elsewhere herein. Identifiers may be constructed using any method described elsewhere herein. Stored data may be copied and accessed using any method described elsewhere herein.

[0061] The identifier may comprise information relating to a location of the encoded symbol, a value of the encoded symbol, or both the location and the value of the encoded symbol. An identifier may include information relating to a location of the encoded symbol and the presence or absence of the identifier in an identifier library may indicate the value of the symbol. The presence of an identifier in an identifier library may indicate a first symbol value (e.g., first bit value) in a binary string and the absence of an identifier in an identifier library may indicate a second symbol value (e.g., second bit value) in a binary string. In a binary system, basing a bit value on the presence or absence of an identifier in an identifier library may reduce the number of identifiers assembled and, therefore, reduce the write time. In an example, the presence of an identifier may indicate a bit value of ‘ 1’ at the mapped location and the absence of an identifier may indicate a bit value of ‘0’ at the mapped location.

[0062] Generating symbols (e.g., bit values) for a piece of information may include identifying the presence or absence of the identifier that the symbol (e.g., bit) may be mapped or encoded to. Determining the presence or absence of an identifier may include sequencing the present identifiers or using a hybridization array to detect the presence of an identifier. In an example, decoding and reading the encoded sequences may be performed using sequencing platforms. Examples of sequencing platforms are described in U.S. Patent Application Ser. No. 14/465,685 filed August 21, 2014, U.S. Patent Application Ser. No. 13/886,234 filed May 2, 2013, and U.S. Patent Application Ser. No. 12/400,593 filed March 9, 2009, each of which is entirely incorporated herein by reference. [0063] In an example, decoding nucleic acid encoded data may be achieved by base-by-base sequencing of the nucleic acid strands, such as Illumina® Sequencing, or by utilizing a sequencing technique that indicates the presence or absence of specific nucleic acid sequences, such as fragmentation analysis by capillary electrophoresis. The sequencing may employ the use of reversible terminators. The sequencing may employ the use of natural or non-natural (e.g., engineered) nucleotides or nucleotide analogs. Alternatively or in addition to, decoding nucleic acid sequences may be performed using a variety of analytical techniques, including but not limited to, any methods that generate optical, electrochemical, or chemical signals. A variety of sequencing approaches may be used including, but not limited to, polymerase chain reaction (PCR), digital PCR, Sanger sequencing, high-throughput sequencing, sequencing-by-synthesis, single-molecule sequencing, sequencing-by-ligation, RNA-Seq (Illumina), Next generation sequencing, Digital Gene Expression (Helicos), Clonal Single MicroArray (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, or massively-parallel sequencing.

[0064] Various read-out methods can be used to pull information from the encoded nucleic acid. In an example, microarray (or any sort of fluorescent hybridization), digital PCR, quantitative PCR (qPCR), and various sequencing platforms can be further used to read out the encoded sequences and by extension digitally encoded data.

[0065] An identifier library may further comprise supplemental nucleic acid sequences that provide metadata about the information, encrypt or mask the information, or that both provide metadata and mask the information. The supplemental nucleic acids may be identified simultaneously with identification of the identifiers. Alternatively, the supplemental nucleic acids may be identified prior to or after identifying the identifiers. In an example, the supplemental nucleic acids are not identified during reading of the encoded information. The supplemental nucleic acid sequences may be indistinguishable from the identifiers. An identifier index or a key may be used to differentiate the supplemental nucleic acid molecules from the identifiers. [0066] The efficiency of encoding and decoding data may be increased by recoding input bit strings to enable the use of fewer nucleic acid molecules. For example, if an input string is received with a high occurrence of ‘ 111’ substrings, which may map to three nucleic acid molecules (e.g., identifiers) with an encoding method, it may be recoded to a ‘000’ substring which may map to a null set of nucleic acid molecules. The alternate input substring of ‘000’ may also be recoded to ‘ 111’. This method of recoding may reduce the total amount of nucleic acid molecules used to encode the data because there may be a reduction in the number of T’s in the dataset. In this example, the total size of the dataset may be increased to accommodate a codebook that specifies the new mapping instructions. An alternative method for increasing encoding and decoding efficiency may be to recode the input string to reduce the variable length. For example, ‘ 111’ may be recoded to ‘00’ which may shrink the size of the dataset and reduce the number of ‘ l’s in the dataset.

[0067] The speed and efficiency of decoding nucleic acid encoded data may be controlled (e.g., increased) by specifically designing identifiers for ease of detection. For example, nucleic acid sequences (e.g., identifiers) that are designed for ease of detection may include nucleic acid sequences comprising a majority of nucleotides that are easier to call and detect based on their optical, electrochemical, chemical, or physical properties. Engineered nucleic acid sequences may be either single or double stranded. Engineered nucleic acid sequences may include synthetic or unnatural nucleotides that improve the detectable properties of the nucleic acid sequence. Engineered nucleic acid sequences may comprise all natural nucleotides, all synthetic or unnatural nucleotides, or a combination of natural, synthetic, and unnatural nucleotides. Synthetic nucleotides may include nucleotide analogues such as peptide nucleic acids, locked nucleic acids, glycol nucleic acids, and threose nucleic acids. Unnatural nucleotides may include dNaM, an artificial nucleoside containing a 3 -methoxy -2-naphthly group, and d5SICS, an artificial nucleoside containing a 6-methylisoquinoline-l-thi one-2 -yl group. Engineered nucleic acid sequences may be designed for a single enhanced property, such as enhanced optical properties, or the designed nucleic acid sequences may be designed with multiple enhanced properties, such as enhanced optical and electrochemical properties or enhanced optical and chemical properties.

[0068] Engineered nucleic acid sequences may comprise reactive natural, synthetic, and unnatural nucleotides that do not improve the optical, electrochemical, chemical, or physical properties of the nucleic acid sequences. The reactive components of the nucleic acid sequences may enable the addition of a chemical moiety that confers improved properties to the nucleic acid sequence. Each nucleic acid sequence may include a single chemical moiety or may include multiple chemical moieties. Example chemical moieties may include, but are not limited to, fluorescent moieties, chemiluminescent moieties, acidic or basic moieties, hydrophobic or hydrophilic moieties, and moieties that alter oxidation state or reactivity of the nucleic acid sequence.

[0069] A sequencing platform may be designed specifically for decoding and reading information encoded into nucleic acid sequences. The sequencing platform may be dedicated to sequencing single or double stranded nucleic acid molecules. The sequencing platform may decode nucleic acid encoded data by reading individual bases (e.g., base-by-base sequencing) or by detecting the presence or absence of an entire nucleic acid sequence (e.g., component) incorporated within the nucleic acid molecule (e.g., identifier). The sequencing platform may include the use of promiscuous reagents, increased read lengths, and the detection of specific nucleic acid sequences by the addition of detectable chemical moieties. The use of more promiscuous reagents during sequencing may increase reading efficiency by enabling faster base calling which in turn may decrease the sequencing time. The use of increased read lengths may enable longer sequences of encoded nucleic acids to be decoded per read. The addition of detectable chemical moiety tags may enable the detection of the presence or absence of a nucleic acid sequence by the presence or absence of a chemical moiety. For example, each nucleic acid sequence encoding a bit of information may be tagged with a chemical moiety that generates a unique optical, electrochemical, or chemical signal. The presence or absence of that unique optical, electrochemical, or chemical signal may indicate a ‘0’ or a ‘ 1’ bit value. The nucleic acid sequence may comprise a single chemical moiety or multiple chemical moieties. The chemical moiety may be added to the nucleic acid sequence prior to use of the nucleic acid sequence to encode data. Alternatively or in addition to, the chemical moiety may be added to the nucleic acid sequence after encoding the data, but prior to decoding the data. The chemical moiety tag may be added directly to the nucleic acid sequence or the nucleic acid sequence may comprise a synthetic or unnatural nucleotide anchor and the chemical moiety tag may be added to that anchor.

[0070] Unique codes may be applied to minimize or detect encoding and decoding errors. Encoding and decoding errors may occur from false negatives (e.g., a nucleic acid molecule or identifier not included in a random sampling). An example of an error detecting code may be a checksum sequence that counts the number of identifiers in a contiguous set of possible identifiers that is included in the identifier library. While reading the identifier library, the checksum may indicate how many identifiers from that contiguous set of identifiers to expect to retrieve, and identifiers can continue to be sampled for reading until the expected number is met. In some implementations, a checksum sequence may be included for every contiguous set of R identifiers where R can be equal in size or greater than 1, 2, 5, 10, 50, 100, 200, 500, or 1000 or less than 1000, 500, 200, 100, 50, 10, 5, or 2. The smaller the value of R, the better the error detection. In some implementations, the checksums may be supplemental nucleic acid sequences. For example, a set comprising seven nucleic acid sequences (e.g., components) may be divided into two groups, nucleic acid sequences for constructing identifiers with a product scheme (components X1-X3 in layer X and Y1-Y3 in layer Y), and nucleic acid sequences for the supplemental checksums (X4-X7 and Y4-Y7). The checksum sequences X4-X7 may indicate whether zero, one, two, or three sequences of layer X are assembled with each member of layer Y. Alternatively, the checksum sequences Y4-Y7 may indicate whether zero, one, two, or three sequences of layer Y are assembled with each member of layer X. In this example, an original identifier library with identifiers {XI Yl, XI Y3, X2Y1, X2Y2, X2Y3} may be supplemented to include checksums to become the following pool: {XI Yl, XI Y3, X2Y1, X2Y2, X2Y3, XI Y6, X2Y7, X3Y4, X6Y1, X5Y2, X6Y3}. The checksum sequences may also be used for error correction. For example, absence of X1Y1 from the above dataset and the presence of X1Y6 and X6Y1 may enable inference that the XI Yl nucleic acid molecule is missing from the dataset. The checksum sequences may indicate whether identifiers are missing from a sampling of the identifier library or an accessed portion of the identifier library. In the case of a missing checksum sequence, access methods such as PCR or affinity tagged probe hybridization may amplify and/or isolate it. In some implementations, the checksums may not be supplemental nucleic acid sequences. They checksums may be coded directly into the information such that they are represented by identifiers.

[0071] Noise in data encoding and decoding may be reduced by constructing identifiers palindromically, for example, by using palindromic pairs of components rather than single components in the product scheme. Then the pairs of components from different layers may be assembled to one another in a palindromic manner (e.g., YXY instead of XY for components X and Y). This palindromic method may be expanded to larger numbers of layers (e.g., ZYXYZ instead of XYZ) and may enable detection of erroneous cross reactions between identifiers. [0072] Adding supplemental nucleic acid sequences in excess (e.g., vast excess) to the identifiers may prevent sequencing from recovering the encoded identifiers. Prior to decoding the information, the identifiers may be enriched from the supplemental nucleic acid sequences. For example, the identifiers may be enriched by a nucleic acid amplification reaction using primers specific to the identifier ends. Alternatively, or in addition to, the information may be decoded without enriching the sample pool by sequencing (e.g., sequencing by synthesis) using a specific primer. In both decoding methods, it may be difficult to enrich or decode the information without having a decoding key or knowing something about the composition of the identifiers.

Alternative access methods may also be employed such as using affinity tag based probes.

Systems for encoding binary sequence data

[0073] A system for encoding digital information into nucleic acids (e.g., DNA) can comprise systems, methods and devices for converting files and data (e.g., raw data, compressed zip files, integer data, and other forms of data) into bytes and encoding the bytes into segments or sequences of nucleic acids, typically DNA, or combinations thereof.

[0074] In an aspect, the present disclosure provides systems for encoding binary sequence data using nucleic acids. A system for encoding binary sequence data using nucleic acids may comprise a device and one or more computer processors. The device may be configured to construct an identifier library. The one or more computer processors may be individually or collectively programmed to (i) translate the information into a sting of symbols, (ii) map the string of symbols to the plurality of identifiers, and (iii) construct an identifier library comprising at least a subset of a plurality of identifiers. An individual identifier of the plurality of identifiers may correspond to an individual symbol of the string of symbols. An individual identifier of the plurality of identifiers may comprise one or more components. An individual component of the one or more components may comprise a nucleic acid sequence.

[0075] In another aspect, the present disclosure provides systems for reading binary sequence data using nucleic acids. A system for reading binary sequence data using nucleic acids may comprise a database and one or more computer processors. The database may store an identifier library encoding the information. The one or more computer processors may be individually or collectively programmed to (i) identify the identifiers in the identifier library, (ii) generate a plurality of symbols from identifiers identified in (i), and (iii) compile the information from the plurality of symbols. The identifier library may comprise a subset of a plurality of identifiers. Each individual identifier of the plurality of identifiers may correspond to an individual symbol in a string of symbols. An identifier may comprise one or more components. A component may comprise a nucleic acid sequence.

[0076] Non-limiting implementations of methods for using the system to encode digital data can comprise steps for receiving digital information in the form of byte streams. Parsing the byte streams into individual bytes, mapping the location of a bit within the byte using a nucleic acid index (or identifier rank), and encoding sequences corresponding to either bit values of 1 or bit values of 0 into identifiers. Steps for retrieving digital data can comprise sequencing a nucleic acid sample or nucleic acid pool comprising sequences of nucleic acid (e.g., identifiers) that map to one or more bits, referencing an identifier rank to confirm if the identifier is present in the nucleic acid pool and decoding the location and bit-value information for each sequence into a byte comprising a sequence of digital information.

[0077] Systems for encoding, writing, copying, accessing, reading, and decoding information encoded and written into nucleic acid molecules may be a single integrated unit or may be multiple units configured to execute one or more of the aforementioned operations. A system for encoding and writing information into nucleic acid molecules (e.g., identifiers) may include a device and one or more computer processors. The one or more computer processors may be programmed to parse the information into strings of symbols (e.g., strings of bits). The computer processor may generate an identifier rank. The computer processor may categorize the symbols into two or more categories. One category may include symbols to be represented by a presence of the corresponding identifier in the identifier library and the other category may include symbols to be represented by an absence of the corresponding identifiers in the identifier library. The computer processor may direct the device to assemble the identifiers corresponding to symbols to be represented to the presence of an identifier in the identifier library.

[0078] The device may comprise a plurality regions, sections, or partitions. The reagents and components to assemble the identifiers may be stored in one or more regions, sections, or partitions of the device. Layers may be stored in separate regions of section of the device. A layer may comprise one or more unique components. The component in one layer may be unique from the components in another layer. The regions or sections may comprise vessels and the partitions may comprise wells. Each layer may be stored in a separate vessel or partition. Each reagent or nucleic acid sequence may be stored in a separate vessel or partition. Alternatively, or in addition to, reagents may be combined to form a master mix for identifier construction. The device may transfer reagents, components, and templates from one section of the device to be combined in another section. The device may provide the conditions for completing the assembly reaction. For example, the device may provide heating, agitation, and detection of reaction progress. The constructed identifiers may be directed to undergo one or more subsequent reactions to add barcodes, common sequences, variable sequences, or tags to one or more ends of the identifiers. The identifiers may then be directed to a region or partition to generate an identifier library. One or more identifier libraries may be stored in each region, section, or individual partition of the device. The device may transfer fluid (e.g., reagents, components, templates) using pressure, vacuum, or suction.

[0079] The identifier libraries may be stored in the device or may be moved to a separate database. The database may comprise one or more identifier libraries. The database may provide conditions for long term storage of the identifier libraries (e.g., conditions to reduce degradation of identifiers). The identifier libraries may be stored in a powder, liquid, or solid form. Aqueous solutions of identifiers may be lyophilized for more stable storage. Alternatively, identifiers may be stored in the absence of oxygen (e.g. anaerobic storage conditions). The database may provide Ultra-Violet light protection, reduced temperature (e.g., refrigeration or freezing), and protection from degrading chemicals and enzymes. Prior to being transferred to a database, the identifier libraries may be lyophilized or frozen. The identifier libraries may include ethylenediaminetetraacetic acid (EDTA) to inactivate nucleases and/or a buffer to maintain the stability of the nucleic acid molecules. [0080] The database may be coupled to, include, or be separate from a device that writes the information into identifiers, copies the information, accesses the information, or reads the information. A portion of an identifier library may be removed from the database prior to copying, accessing or reading. The device that copies the information from the database may be the same or a different device from that which writes the information. The device that copies the information may extract an aliquot of an identifier library from the device and combine that aliquot with the reagents and constituents to amplify a portion of or the entire identifier library. The device may control the temperature, pressure, and agitation of the amplification reaction. The device may comprise partitions and one or more amplification reaction may occur in the partition comprising the identifier library. The device may copy more than one pool of identifiers at a time.

[0081] The copied identifiers may be transferred from the copy device to an accessing device. The accessing device may be the same device as the copy device. The access device may comprise separate regions, sections, or partitions. The access device may have one or more columns, bead reservoirs, or magnetic regions for separating identifiers bound to affinity tags. Alternatively, or in addition to, the access device may have one or more size selection units. A size selection unit may include agarose gel electrophoresis or any other method for size selecting nucleic acid molecules. Copying and extraction may be performed in the same region of a device or in different regions of a device.

[0082] The accessed data may be read in the same device or the accessed data may be transferred to another device. The reading device may comprise a detection unit to detect and identify the identifiers. The detection unit may be part of a sequencer, hybridization array, or other unit for identifying the presence or absence of an identifier. A sequencing platform may be designed specifically for decoding and reading information encoded into nucleic acid sequences. The sequencing platform may be dedicated to sequencing single or double stranded nucleic acid molecules. The sequencing platform may decode nucleic acid encoded data by reading individual bases (e.g., base-by-base sequencing) or by detecting the presence or absence of an entire nucleic acid sequence (e.g., component) incorporated within the nucleic acid molecule (e.g., identifier). Alternatively, the sequencing platform may be a system such as Illumina® Sequencing or fragmentation analysis by capillary electrophoresis. Alternatively or in addition to, decoding nucleic acid sequences may be performed using a variety of analytical techniques implemented by the device, including but not limited to, any methods that generate optical, electrochemical, or chemical signals.

[0083] Information storage in nucleic acid molecules may have various applications including, but not limited to, long term information storage, sensitive information storage, and storage of medical information. In an example, a person’s medical information (e.g., medical history and records) may be stored in nucleic acid molecules and carried on his or her person. The information may be stored external to the body (e.g., in a wearable device) or internal to the body (e.g., in a subcutaneous capsule). When a patient is brought into a medical office or hospital, a sample may be taken from the device or capsule and the information may be decoded with the use of a nucleic acid sequencer. Personal storage of medical records in nucleic acid molecules may provide an alternative to computer and cloud based storage systems. Personal storage of medical records in nucleic acid molecules may reduce the instance or prevalence of medical records being hacked. Nucleic acid molecules used for capsule-based storage of medical records may be derived from human genomic sequences. The use of human genomic sequences may decrease the immunogenicity of the nucleic acid sequences in the event of capsule failure and leakage.

Chemical methods for nucleic acid-based data storage

[0084] In an aspect, the present disclosure provides a method for writing information into a nucleic acid sequence, comprising: (a) generating a string of symbols to represent the information; (b) constructing a plurality of components, wherein each individual component of the plurality of components comprises a nucleic acid sequence; (c) generating at least one sticky end of the individual component of the plurality of components; (d) chemically linking together two or more components of the plurality of components via the at least one sticky end of the individual component of the two or more components, thereby generating a plurality of identifiers, wherein each identifier of the plurality of identifiers comprises two or more components, wherein an individual identifier of the plurality of identifiers corresponds to an individual symbol in the string of symbols; and (e) selectively capturing or amplifying an identifier library comprising at least a subset of the plurality of identifiers.

[0085] In some embodiments, each symbol of the string of symbols is one of one or more possible symbol values. In some embodiments, each symbol in the string of symbols is one of two possible symbol values. In some embodiments, one symbol value at each position of the string of symbols may be represented by the absence of a distinct identifier in the identifier library. In some embodiments, the two possible symbol values are a bit-value of 0 and 1, wherein the individual symbol with the bit-value of 0 in the string of symbols may be represented by an absence of a distinct identifier in the identifier library, wherein the individual symbol with the bit-value of 1 in the string of symbols may be represented by a presence of the distinct identifier in the identifier library, or vice versa.

[0086] In some embodiments, (d) comprises chemically linking the two or more components from two or more layers and wherein each layer of the two or more layers comprises a distinct set of components. In some embodiments, the individual identifier from the identifier library comprises one component from each layer of the two or more layers. In some embodiments, the two or more components are assembled in a fixed order. In some embodiments, the two or more components are assembled in any order. In some embodiments, the two or more components are assembled with one or more partitioning components disposed between two components from different layers of the two or more layers. In some embodiments, the individual identifier comprises one component from each layer of a subset of the two or more layers. In some embodiments, the individual identifier comprises at least one component from each of the two or more layers.

[0087] In some embodiments, (c) comprises using an endonuclease to generate the at least one sticky end of the individual component of the plurality of components. In some embodiments, the at least one sticky end is at a 5' end of the individual component. In some embodiments, the at least one sticky end is at a 3' end of the individual component. In some embodiments, (c) comprises generating two sticky ends of the individual component. In some embodiments, the at least one sticky end is at least one nucleotide in length. In some embodiments, the at least one sticky end is six nucleotides in length.

[0088] In some embodiments, the plurality of nucleic acid sequences stores metadata of the information or conceals the information. In some embodiments, two or more identifier libraries are combined and wherein each identifier library of the two or more identifier libraries is tagged with a distinct barcode. In some embodiments, each individual identifier in the identifier library comprises a distinct barcode or a subset identifiers of the identifier library comprises a distinct barcode. In some embodiments, the plurality of identifiers, or the plurality of components that comprise the identifiers, is selected for ease of read, write, access, copy, and deletion operations. [0089] In some embodiments, chemically linking comprises ligating together two or more components of the plurality of components using a reagent comprising a ligase. In some embodiments, the ligase is a T4 ligase, a T7 ligase, a T3 ligase, or an E. coli ligase. In some embodiments, the reagent further comprises an additive. In some embodiments, the additive increases efficiency of the ligase. In some embodiments, the additive comprises polyethylene glycol (PEG). In some embodiments, the PEG is PEG400, PEG6000, PEG8000 or any combination thereof. In some embodiments, a final concentration of the PEG molecules is at least about 1% weight per volume (w/v). In some embodiments, a reaction time of the ligating is at least one minute. In some embodiments, the ligating is at 30 degrees Celsius or higher. In some embodiments, a reaction efficiency of the ligating is at least about 20%. In some embodiments, the method further comprises inactivating the ligase using a buffer containing EDTA or guanidine thiocyanate. In some embodiments, final concentration of the ligase is at least about 5 CEU/pL. In some embodiments, the reagent further comprises glycerol molecules.

[0090] In some embodiments, chemically linking in (d) comprises using overlap-extension polymerase chain reaction (PCR). In some embodiments, the individual component is a deoxyribonucleic acid (DNA) or a ribonucleic acid. In some embodiments, the individual component has been rehydrated. In some embodiments, the individual component is rehydrated from a dehydrated component. In some embodiments, the method further comprises dehydrating the identifier library by dehydrating each individual identifier of at least the subset of the plurality of identifiers. In some embodiments, each individual identifier of at least the subset of the plurality of identifiers is dehydrated. In some embodiments, the method further comprises rehydrating each individual identifier of at least the subset of the plurality of identifiers. In some embodiments, the method further comprises adding a preserving additive to the identifier library to prevent identifier degradation.

[0091] In some embodiments, the plurality of identifiers is copied with PCR. In some embodiments, the PCR has at least 10 cycles. In some embodiments, the plurality of identifiers is amplified with PCR up to a concentration 10 nanograms per microliter. In some embodiments, the PCR is an emulsion PCR. In some embodiments, the plurality of identifiers is copied with linear amplification. In some embodiments, after the PCR, linear amplification is used to create more copies of the plurality of identifiers. In some embodiments, a subset of the plurality of identifiers is accessed with one or more PCR reactions. In some embodiments, a subset of the plurality of identifiers is accessed with one or more affinity tagged probes.

[0092] In some embodiments, identifiers of the subset of the plurality of identifiers have a set of components in common. In some embodiments, the identifiers are purified by gel electrophoresis. In some embodiments, the identifiers are purified by affinity tagged probes. In some embodiments, the identifiers are amplified using PCR. In some embodiments, the identifiers are designed to avoid thymine-thymine dinucleotides or cytosine-cytosine dinucleotides.

Chemical methods for assembling components

[0093] Reactions and methods provided herein can be used in systems described herein for assembling identifiers from one or more components. For example, different reaction mixtures for different chemical methods provided herein can be used in the finisher of the system to assemble different components.

A. Overlap extension PCR (OEPCR) assembly

[0094] In OEPCR, components can be assembled in a reaction comprising polymerase and dNTPs (deoxynucleotide tri phosphates comprising dATP, dTTP, dCTP, dGTP or variants or analogs thereof). Components can be single stranded or double stranded nucleic acids. Components to be assembled adjacent to each other may have complementary 3' ends, complementary 5' ends, or homology between one component's 5' end and the adjacent component's 3' end. These end regions, termed "hybridization regions", are intended to facilitate the formation of hybridized junctions between the components during OEPCR, wherein the 3' end of one input component (or its complement) is hybridized to the 3' end of its intended adjacent component (or its complement). An assembled double-stranded product is then formed by polymerase extension. This product may then be assembled to more components through subsequent hybridization and extension.

[0095] In some implementations, the OEPCR may comprise cycling between three temperatures: a melting temperature, an annealing temperature, and an extension temperature. The melting temperature is intended to turn double stranded nucleic acids into single stranded nucleic acids, as well as remove the formation of secondary structures or hybridizations within a component or between components. Typically the melting temperature is high, for example above 95 degrees Celsius. In some implementations the melting temperature may be at least 96, 97, 98, 99, 100, 101, 102, 103, 104, or at least 105 degrees Celsius. In other implementations, the melting temperature may be at most 95, 94, 93, 92, 91, or at most 90 degrees Celsius. A higher melting temperature will improve dissociation of nucleic acids and their secondary structures, but may also cause side effects such as the degradation of nucleic acids or the polymerase. Melting temperatures may be applied to the reaction for at least 1, 2, 3, 4, or at least 5 seconds, or above, such as 30 seconds, 1 minute, 2 minutes, or 3 minutes.

[0096] The annealing temperature is intended to facilitate the formation of hybridization between complementary 3' ends of intended adjacent components (or their complements). In some implementations, the annealing temperature may match the calculated melting temperature of the intended hybridized nucleic acid formation. In other implementations, the annealing temperature may be within 10 degrees Celsius or more of said melting temperature. In some implementations, the annealing temperature may be at least 25, 30, 50, 55, 60, 65, or at least 70 degrees Celsius. The melting temperature may depend on the sequence of the intended hybridization region between components. Longer hybridization regions have higher melting temperatures, and hybridization regions with higher percent content of Guanine or Cytosine nucleotides may have higher melting temperatures. It may therefore be possible to design components for OEPCR reactions intended to assemble optimally at particular annealing temperatures. Annealing temperatures may be applied to the reaction for at least 1, 5, 10, 15, 20, 25, or at least 30 seconds, or above.

[0097] The extension temperature is intended to initiate and facilitate the nucleic acid chain elongation of hybridized 3' ends catalyzed by one or more polymerase enzymes. In some implementations, the extension temperature may be set at the temperature in which the polymerase functions optimally in terms of nucleic acid binding strength, elongation speed, elongation stability, or fidelity. In some implementations, the extension temperature may be at least 30, 40, 50, 60, or at least 70 degrees Celsius, or above. Annealing temperatures may be applied to the reaction for at least 1, 5, 10, 15, 20, 25, 30, 40, 50, or at least 60 seconds or above. Recommended extension times may be around 15 to 45 seconds per kilobase of expected elongation.

[0098] In some implementations of OEPCR, the annealing temperature and the extension temperature may be the same. Thus a 2-step temperature cycle may be used instead of a 3 -step temperature cycle. Examples of combined annealing and extension temperatures include 60, 65, or 72 degrees Celsius.

[0099] In some implementations, OEPCR may be performed with one temperature cycle. Such implementations may involve the intended assembly of just two components. In other implementations, OEPCR may be performed with multiple temperature cycles. Any given nucleic acid in OEPCR may only assemble to at most one other nucleic acid in one cycle. This is because assembly (or extension or elongation) may only occurs at the 3' end of a nucleic acid and each nucleic acid only has one 3' end. Therefore, the assembly of multiple components may require multiple temperature cycles. For example, assembling four components may involve 3 temperature cycles. Assembling 6 components may involve 5 temperature cycles. Assembling 10 components may involve 9 temperature cycles. In some implementations, using more temperature cycles than the minimum required may increase assembly efficiency. For example using four temperature cycles to assemble two components may yield more product than only using one temperature cycle. This is because the hybridization and elongation of components is a statistical event that occurs with a fraction of the total number of components in each cycle. So the total fraction of assembled components may increase with increased cycles.

[0100] In addition to temperature cycling considerations, the design of the nucleic acid sequences in OEPCR may influence the efficiency of their assembly to one another. Nucleic acids with long hybridization regions may hybridize more efficiently at a given annealing temperature compared with nucleic acids with short hybridization regions. This is because a longer hybridized product contains a larger number of stable base-pairs and may therefore be a more stable overall hybridized product than a shorter hybridized product. Hybridization regions may have a length of at least 1, 2, 3 4, 5, 6, 7, 8, 9, or at least 10, or more bases.

[0101] Hybridization regions with high guanine or cytosine content may hybridize more efficiently at a given temperature than hybridization regions with low guanine or cytosine content. This is because guanine forms a more stable base-pair with cytosine than adenine does with thymine. Hybridization regions may have a guanine or cytosine content (also known as GC content) of anywhere from 0% to 100%. For example, hybridization regions may have a guanine or cytosine content from 0% to 5%, from 5% to 10%, from 10% to 15%, from 15% to 20%, from

20% to 25%, from 25% to 30%, from 30% to 35%, from 35% to 40%, from 40% to 45%, from

45% to 50%, from 50% to 55%, from 55% to 60%, from 60% to 65%, from 65% to 70%, from

70% to 75%, from 75% to 80%, from 80% to 85%, from 85% to 90%, from 90% to 95%, or from

95% to 100%.

[0102] In addition to hybridization region length and GC content, there are many more aspects of the nucleic acid sequence design that may affect the efficiency of the OEPCR. For example, the formation of undesired secondary structures within a component may interfere with its ability to form a hybridization product with its intended adjacent component. These secondary structures may include hairpin loops. The types of possible secondary structures and their stability (for example meting temperature) for a nucleic acid may be predicted based on the sequence. Design space search algorithms may be used to determine nucleic acid sequences that meet proper length and GC content criteria for efficient OEPCR, while avoiding sequences with potentially inhibitory secondary structures. Design space search algorithms may include genetic algorithms, heuristic search algorithms, meta-heuristic search strategies like tabu search, branch-and-bound search algorithms, dynamic programming-based algorithms, constrained combinatorial optimization algorithms, gradient descent-based algorithms, randomized search algorithms, or combinations thereof. [0103] Likewise, the formation of homodimers (nucleic acid molecules that hybridize with nucleic acid molecules of the same sequence) and unwanted heterodimers (nucleic acid sequences that hybridize with other nucleic acid sequences aside from their intended assembly partner) may interfere with OEPCR. Similar to secondary structures within a nucleic acid, the formation of homodimers and heterodimers may be predicted and accounted for during nucleic acid design using computation methods and design space search algorithms.

[0104] Longer nucleic acid sequences or higher GC content may create increased formation of unwanted secondary structures, homodimers, and heterodimers with the OEPCR. Therefore, in some implementations, the use of shorter nucleic acid sequences or lower GC content may lead to higher assembly efficiency. These design principles may counteract the design strategies of using long hybridization regions or high GC content for more efficient assembly. As such, in some implementations, OEPCR may be optimized by using long hybridization regions with high GC content but short non-hybridization regions with low GC content. The overall length of nucleic acids may be at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or at least 100 bases, or above. In some implementations, there may be an optimal length and optimal GC content for the hybridization regions of nucleic acids where the assembly efficiency is optimized.

[0105] A larger number of distinct nucleic acids in an OEPCR reaction may interfere with the expected assembly efficiency. This is because a larger number of distinct nucleic acid sequences may create a higher probability for undesirable molecular interactions, particularly in the form of heterodimers. Therefore in some implementations of OEPCR that assemble large numbers of components, nucleic acid sequence constraints may become more stringent for efficient assembly.

[0106] Primers for amplifying the anticipated final assembled product may be included in an OEPCR reaction. The OEPCR reaction may then be performed with more temperature cycles to improve the yield of the assembled product, not just by creating more assemblies between the constituent components, but also by exponentially amplifying the full assembled product in the manner of conventional PCR.

[0107] Additives may be included in the OEPCR reaction to improve assembly efficiency. For example, the addition of Betaine, Dimethyl sulfoxide (DMSO), non-ionic detergents, Formamide, Magnesium, Bovine Serum Albumin (BSA), or combinations thereof. Additive content (weight per volume) may be at least 0%, 1%, 5%, 10%, or at least 20%, or more.

[0108] Various polymerases may be used for OEPCR. The polymerase can be naturally occurring or synthesized. An example polymerase is a 29 polymerase or derivative thereof. In some cases, a transcriptase or a ligase is used (i.e., enzymes which catalyze the formation of a bond) in conjunction with polymerases or as an alternative to polymerases to construct new nucleic acid sequences. Examples of polymerases include a DNA polymerase, a RNA polymerase, a thermostable polymerase, a wild-type polymerase, a modified polymerase, E. coli DNA polymerase I, T7 DNA polymerase, bacteriophage T4 DNA polymerase 29 (phi29) DNA polymerase, Taq polymerase, Tth polymerase, Tli polymerase, Pfu polymerase Pwo polymerase, VENT polymerase, DEEPVENT polymerase, Ex-Taq polymerase, LA-Taw polymerase, Sso polymerase Poc polymerase, Pab polymerase, Mth polymerase ES4 polymerase, Tru polymerase, Tac polymerase, Tne polymerase, Tma polymerase, Tea polymerase, Tih polymerase, Tfi polymerase, Platinum Taq polymerases, Tbr polymerase, Phusion polymerase, KAPA polymerase, Q5 polymerase, Tfl polymerase, Pfutubo polymerase, Pyrobest polymerase, KOD polymerase, Bst polymerase, Sac polymerase, KI enow fragment polymerase with 3’ to 5’ exonuclease activity, and variants, modified products and derivatives thereof. Different polymerases may be stable and function optimally at different temperatures. Moreover, different polymerases have different properties. For example, some polymerases, such a Phusion polymerase, may exhibit 3' to 5' exonuclease activity, which may contribute to higher fidelity during nucleic acid elongation. Some polymerases may displace leading sequences during elongation, while others may degrade them or halt elongation. Some polymerases, like Taq, incorporate an adenine base at the 3' end of nucleic acid sequences. This process is referred to as A-tailing and may be inhibitory to OEPCR as the addition of an Adenine base may disrupt the designed 3' complementarity between intended adjacent components. OEPCR may also be referred to as polymerase cycling assembly (or PCA).

B. Ligation assembly

[0109] In ligation assembly, separate nucleic acids are assembled in a reaction comprising one or more ligase enzymes and additional co-factors. Co-factors may include Adenosine Tri-Phosphate (ATP), Dithiothreitol (DTT), or Magnesium ion (Mg2+). During ligation, the 3 '-end of one nucleic acid strand is covalently linked to the 5' end of another nucleic acid strand, thus forming an assembled nucleic acid. Components in a ligation reaction may be blunt-ended double stranded DNA (dsDNA), single stranded DNA (ssDNA), or partially hybridized single-stranded DNA. Strategies that bring the ends of nucleic acids together increase the frequency of viable substrate for ligase enzymes, and thus may be used for improving the efficiency of ligase reactions. Blunt-ended dsDNA molecules tend to form hydrophobic stacks on which ligase enzymes may act, but a more successful strategy for bringing nucleic acids together may be to use nucleic acid components with either 5' or 3' single-stranded overhangs that have complementarity for the overhangs of components to which they are intended to assemble. In the latter instance, more stable nucleic acid duplexes may form due to base-base hybridization.

[0110] When a double stranded nucleic acid has an overhang strand on one end, the other strand on the same end may be referred to as a "cavity". Together, a cavity and overhang form a "sticky end", also known as a "cohesive-end". A sticky end may be either a 3' overhang and a 5' cavity, or a 5' overhang and a 3' cavity. The sticky-ends between two intended adjacent components may be designed to have complementarity such that the overhang of both sticky ends hybridize such that each overhang ends directly adjacent to the beginning of the cavity on the other component. This forms a "nick" (a double stranded DNA break) that may be "sealed" (covalently linked through a phosphodiester bond) by the action of a ligase. Either the nick on one strand or the other, or both, may be sealed. Thermodynamically, the top and bottom strand of a molecule that forms a sticky end may move between associated and dissociated states, and therefore the sticky end may be a transient formation. Once, however, the nick along one strand of a sticky end duplex between two components is sealed, that covalent linkage remains even if the members of the opposite strand dissociate. The linked strand may then become a template to which the intended adjacent members of the opposite strand can bind and once again form a nick that may be sealed.

[0111] Sticky ends may be created by digesting dsDNA with one or more endonucleases. Endonucleases (that may be referred to as restriction enzymes) may target specific sites (that may be referred to as restriction sites) on either or both ends of dsDNA molecule, and create a staggered cleavage (sometimes referred to as a digestion) thus leaving a sticky end. The digest may leave a palindromic overhang (an overhang with a sequence that is the reverse complement of itself). If so, then two components digested with the same endonuclease may form complimentary sticky ends along which they may be assembled with a ligase. The digestion and ligation may occur together in the same reaction if the endonuclease and ligase are compatible. The reaction may occur at a uniform temperature, such as 4, 10, 16, 25, or 37 degrees Celsius. Or the reaction may cycle between multiple temperatures, such as between 16 degrees Celsius and 37 degrees Celsius. Cycling between multiple temperatures may enable the digestion and ligation to each proceed at their respective optimal temperatures during different parts of the cycle.

[0112] It may be beneficial to perform the digestion and ligation in separate reactions. For example, if the desired ligases and the desired endonucleases function optimally at different conditions. Or, for example, if the ligated product forms a new restriction site for the endonuclease. In these instances, it may be better to perform the restriction digest and then the ligation separately, and perhaps it may be further beneficial to remove the restriction enzyme prior to ligation. Nucleic acids may be separated from enzymes through phenol-chloroform extraction, ethanol precipitation, magnetic bead capture, and/or silica membrane adsorption, washing, and elution. Multiple endonucleases may be used in the same reaction, though care should be taken to ensure that the endonucleases do not interfere with each other and function under similar reaction conditions. Using two endonucleases, one may create orthogonal (non- complementary) sticky ends on both ends of a dsDNA component.

[0113] Endonuclease digestion will leave sticky ends with phosphorylated 5' ends. Ligases may only function on phosphorylated 5' ends, and not on non-phosphorylated 5' ends. As such, there may not be any need for an intermediate 5' phosphorylation step in between digestion and ligation. A digested dsDNA component with a palindromic overhang on its sticky end may ligate to itself. To prevent self-ligation, it may be beneficial to dephosphorylate said dsDNA component prior to ligation.

[0114] Multiple endonucleases may target different restriction sites, but leave compatible overhangs (overhangs that are the reverse complement of each other). The product of ligation of sticky ends created with two such endonucleases may result in an assembled product that does not contain a restriction site for either endonuclease at the site of ligation. Such endonucleases form the basis of assembly methods, such as biobricks assembly, that may programmably assemble multiple components using just two endonucleases by performing repetitive digestionligation cycles. FIG. 20 illustrates an example of a digestion-ligation cycle using endonucleases BamHI and Bglll with compatible overhangs.

[0115] In some implementations, the endonucleases used to create sticky ends may be type IIS restriction enzymes. These enzymes cleave a fixed number of bases away from their restriction sites in a particular direction, therefore the sequence of the overhangs that they generate may be customized. The overhang sequences need not be palindromic. The same type IIS restriction enzyme may be used to create multiple different sticky ends in the same reaction, or in multiple reactions. Moreover, one or multiple type IIS restriction enzymes may be used to create components with compatible overhangs in the same reaction, or in multiple reactions. The ligation site between two sticky ends generated by type IIS restriction enzymes may be designed such that it does not form a new restriction site. In addition, the type IIS restriction enzyme sites may be placed on a dsDNA such that the restriction enzyme cleaves off its own restriction site when it generates a component with a sticky end. Therefore the ligation product between multiple components generated from type IIS restriction enzymes may not contain any restriction sites.

[0116] Type IIS restriction enzymes may be mixed in a reaction together with ligase to perform the component digestion and ligation together. The temperature of the reaction may be cycled between two or more values to promote optimal digestion and ligation. For example, the digestion may be performed optimally at 37 degrees Celsius and the ligation may be performed optimally at 16 degrees Celsius. More generally, the reaction may cycle between temperature values of at least 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, or at least 65 degrees Celsius or above. A combined digestion and ligation reaction may be used to assemble at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 components, or more. Examples of assembly reactions that leverage Type IIS restriction enzymes to create sticky ends include Golden Gate Assembly (also known as Golden Gate Cloning) or Modular Cloning (also known as MoClo). [0117] In some implementations of ligation, exonucleases may be used to create components with sticky ends. 3' exonucleases may be used to chew back the 3' ends from dsDNA, thus creating 5' overhangs. Likewise, 5' exonucleases may be used to chew back the 5' ends from dsDNA thus creating 3' overhangs. Different exonucleases may have different properties. For example, exonucleases may differ in the direction of their nuclease activity (5' to 3' or 3' to 5'), whether or not they act on ssDNA, whether they act on phosphorylated or non-phosphorylated 5' ends, whether or not they are able to initiate on a nick, or whether or not they are able to initiate their activity on 5' cavities, 3' cavities, 5' overhangs, or 3' overhangs. Different types of exonucleases include Lambda exonuclease, RecJf, Exonuclease III, Exonuclease I, Exonuclease T, Exonuclease V, Exonuclease VIII, Exonuclease VII, Nuclease BAL 31, T5 Exonuclease, and

T7 Exonuclease. [0118] Exonuclease may be used in a reaction together with ligase to assemble multiple components. The reaction may occur at a fixed temperature or cycle between multiple temperatures, each ideal for the ligase or the exonuclease, respectively. Polymerase may be included in an assembly reaction with ligase and a 5'-to-3' exonuclease. The components in such a reaction may be designed such that components intended to assemble adjacent to each other share homologous sequences on their edges. For example, a component X to be assembled with component Y may have a 3' edge sequence of the form 5'-z-3', and the component Y may have a 5' edge sequence of the form 5'-z-3', where z is any nucleic acid sequence. We refer to homologous edge sequences of such a form as 'gibson overlaps'. As the 5' exonuclease chews back the 5' end of dsDNA components with gibson overlaps it creates compatible 3' overhangs that hybridize to each other. The hybridized 3' ends may then be extended by the action of polymerase to the end of the template component, or to the point where the extended 3' overhang of one component meets the 5' cavity of the adjacent component, thereby forming a nick that may be sealed by a ligase. Such an assembly reaction where polymerase, ligase, and exonuclease are used together is often referred to as "Gibson assembly". Gibson assembly may be performed by using T5 exonuclease, Phusion polymerase, and Taq ligase, and incubating the reaction at 50 degrees Celsius. In said instance, the use of the thermophilic ligase, Taq, enables the reaction to proceed at 50 degrees Celsius, a temperature suitable for all three types of enzymes in the reaction.

[0119] The term "Gibson assembly" may generally refer to any assembly reaction involving polymerase, ligase, and exonuclease. Gibson assembly may be used to assemble at least 2, 3, 4, 5, 6, 7, 8, 9, or at least 10, or more components. Gibson assembly may occur as a one-step, isothermal reaction or as a multi-step reaction with one or more temperature incubations. For example, Gibson assembly may occur at temperatures of at least 30, 40, 50, 60, or at least 70 degrees, or more. The incubation time for a Gibson assembly may be at least 1, 5, 10, 20, 40, or at least 80 minutes. [0120] Gibson assembly reactions may occur optimally when gibson overlaps between intended adjacent components are a certain length and have sequence features, such as sequences that avoid undesirable hybridization events such as hairpins, homodimers, or unwanted heterodimers. Generally, gibson overlaps of at least 20 bases are recommended. But Gibson overlaps may be at least 1, 2, 3, 5, 10, 20, 30, 40, 50, 60, or at least 100, or more bases in length. The GC content of a gibson overlap may be anywhere from 0% to 100%. For example, the GC content of a gibson overlap may be from 0% to 5%, from 5% to 10%, from 10% to 15%, from 15% to 20%, from

20% to 25%, from 25% to 30%, from 30% to 35%, from 35% to 40%, from 40% to 45%, from

45% to 50%, from 50% to 55%, from 55% to 60%, from 60% to 65%, from 65% to 70%, from

70% to 75%, from 75% to 80%, from 80% to 85%, from 85% to 90%, from 90% to 95%, or from

95% to 100%.

[0121] Though Gibson assembly is commonly described with a 5' exonuclease, the reaction may also occur with a 3' exonuclease. As the 3' exonuclease chews back the 3' end of dsDNA components, the polymerase counteracts the action by extending the 3' end. This dynamic process may continue until the 5' overhang (created by the exonuclease) of two components (that share a gibson overlap) hybridize and the polymerase extends the 3' end of one component far enough to meet the 5' end of its adjacent component, thus leaving a nick that may be sealed by a ligase.

[0122] In some implementations of ligation, components with sticky ends may be created synthetically, as opposed to enzymatically, by mixing together two single stranded nucleic acids, or oligos, that do not share full complementarity.

[0123] The index region and hybridization region(s) of oligos in sticky-end ligation may be designed to facilitate the proper assembly of components. Components with long overhangs may hybridize more efficiently with each other at a given annealing temperature compared with components with short overhangs. Overhangs may have a length of at least 1, 2, 3 4, 5, 6, 7, 8, 9,

10, 15, 20, or at least 30, or more bases. [0124] Components with overhangs that contain high guanine or cytosine content may hybridize more efficiently to their complementary component at a given temperature than components with overhangs that contain low guanine or cytosine content. This is because guanine forms a more stable base-pair with cytosine than adenine does with thymine. Overhangs may have a guanine or cytosine content (also known as GC content) of anywhere between 0% and 100%.

[0125] As with overhang sequences, the GC content and length of the index region of an oligo may also affect ligation efficiency. This is because sticky-end components may assemble more efficiently if the top and bottom strand of each component are stably bound. Therefore, index regions may be designed with higher GC content, longer sequences, and other features that promote higher melting temperatures. However, there are many more aspects of the oligo design, for both the index region and overhang sequence(s), that may affect the efficiency of the ligation assembly. For example, the formation of undesired secondary structures within a component may interfere with its ability to form an assembled product with its intended adjacent component. This may occur due to either secondary structures in the index region, in the overhang sequence, or in both. These secondary structures may include hairpin loops. The types of possible secondary structures and their stability (for example meting temperature) for an oligo may be predicted based on the sequence. Design space search algorithms may be used to determine oligo sequences that meet proper length and GC content criteria for the formation of effective components, while avoiding sequences with potentially inhibitory secondary structures. Design space search algorithms may include genetic algorithms, heuristic search algorithms, metaheuristic search strategies like tabu search, branch-and-bound search algorithms, dynamic programming-based algorithms, constrained combinatorial optimization algorithms, gradient descent-based algorithms, randomized search algorithms, or combinations thereof.

[0126] Likewise, the formation of homodimers (oligos that hybridize with oligos of the same sequence) and unwanted heterodimers (oligos that hybridize with other oligos aside from their intended assembly partner) may interfere with ligation. Similar to secondary structures within a component, the formation of homodimers and heterodimers may be predicted and accounted for during oligo design using computation methods and design space search algorithms.

[0127] Longer oligo sequences or higher GC content may create increased formation of unwanted secondary structures, homodimers, and heterodimers within the ligation reaction. Therefore, in some implementations, the use of shorter oligos or lower GC content may lead to higher assembly efficiency. These design principles may counteract the design strategies of using long oligos or high GC content for more efficient assembly. As such, there may be an optimal length and optimal GC content for the oligos that make up each component such that the ligation assembly efficiency is optimized. The overall length of oligos to be used in ligation may be at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or at least 100 bases, or above. The overall GC content of oligos to be used in ligation may be anywhere from 0% to 100%. For example, the overall GC content of oligos to be used in ligation can be from 0% to 5%, from 5% to 10%, from 10% to 15%, from 15% to 20%, from 20% to 25%, from 25% to 30%, from 30% to 35%, from 35% to

40%, from 40% to 45%, from 45% to 50%, from 50% to 55%, from 55% to 60%, from 60% to

65%, from 65% to 70%, from 70% to 75%, from 75% to 80%, from 80% to 85%, from 85% to

90%, from 90% to 95%, or from 95% to 100%.

[0128] In addition to sticky end ligation, ligation may also occur between single-stranded nucleic acids using staple (or template or bridge) strands. This method can be referred to as staple strand ligation (SSL), template directed ligation (TDL), or bridge strand ligation. In TDL, two single stranded nucleic acids hybridize adjacently onto a template, thus forming a nick that may be sealed by a ligase. The same nucleic acid design considerations for sticky end ligation also apply to TDL. Stronger hybridization between the templates and their intended complementary nucleic acid sequences may lead to increased ligation efficiency. Therefore sequence features that improve the hybridization stability (or melting temperature) on each side of the template may improve ligation efficiency. These features may include longer sequence length and higher GC content. The length of nucleic acids in TDL, including templates, may be at least 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or at least 100 bases, or above. The GC content of nucleic acids, including templates, may be anywhere from 0% to 100%. For example, the GC content of nucleic acids, including templates, can be from 0% to 5%, from 5% to 10%, from 10% to 15%, from 15% to

20%, from 20% to 25%, from 25% to 30%, from 30% to 35%, from 35% to 40%, from 40% to

45%, from 45% to 50%, from 50% to 55%, from 55% to 60%, from 60% to 65%, from 65% to

70%, from 70% to 75%, from 75% to 80%, from 80% to 85%, from 85% to 90%, from 90% to

95%, or from 95% to 100%.

[0129] In TDL, as with sticky end ligation, care may be taken to design component and template sequences that avoid unwanted secondary structures by using nucleic acid structure-predicting software with sequence space search algorithms. As the components in TDL may be single stranded instead of double stranded, there may be higher incidence of unwanted secondary structures (as compared to sticky end ligation) due to the exposed bases.

[0130] TDL may also be performed with blunt-ended dsDNA components. In such reactions, in order for the staple strand to properly bridge two single-stranded nucleic acids, the staple may first need to displace or partially displace the full single-stranded complements. To facilitate the TDL reaction with dsDNA components, the dsDNA may initially be melted with incubation at a high temperature. The reaction may then be cooled thus allowing staple strands to anneal to their proper nucleic acid complements. This process may be made even more efficient by using a relatively high concentration of template compared to dsDNA components, thus enabling the templates to outcompete the proper full-length ssDNA complements for binding. Once two ssDNA strands get assembled by their template and a ligase, that assembled nucleic acid may then become a template for the opposite full-length ssDNA complements. Therefore, ligation of blunt-ended dsDNA with TDL may be improved through multiple rounds of melting (incubation at higher temperatures) and annealing (incubation at lower temperatures). This process may be referred to as Ligase Cyling Reaction, or LCR. Proper melting and annealing temperatures depend on the nucleic acid sequences. Melting and annealing temperatures may be at least 4, 10, 20, 20, 30, 40, 50, 60, 70, 80, 90, or 100 degrees Celsius. The number of temperature cycles may be at least 1, 5, 10, 15, 20, 15, 30, or more.

[0131] All ligations may be performed in fixed temperature reactions or in multi-temperature reactions. Ligation temperatures may be at least 0, 4, 10, 20, 20, 30, 40, 50, or 60 degrees Celsius or above. The optimal temperature for ligase activity may differ depending on the type of ligase. Moreover, the rate at which components adjoin or hybridize in the reaction may differ depending on their nucleic acid sequences. Higher incubation temperatures may promote faster diffusion and therefore increase the frequency with which components temporarily adjoin or hybridize. However increased temperature may also disrupt base pair bonds and therefore decrease the stability of those adjoined or hybridized component duplexes. The optimal temperature for ligation may depend on the number of nucleic acids to be assembled, the sequences of those nucleic acids, the type of ligase, as well as other factors such as reaction additives. For example, two sticky end components with 4-base complementary overhangs may be assembled faster at 4 degrees Celsius with T4 ligase than at 25 degrees Celsius with T4 ligase. But two sticky-end components with 25-base complementary overhangs may assemble faster at 25 degrees Celsius with T4 ligase than at 4 degrees Celsius with T4 ligase, and perhaps faster than ligation with 4- base overhangs at any temperature. In some implementations of ligation, it may be beneficial to heat and slowly cool the components for annealing prior to ligase addition.

[0132] Ligation may be used to assemble at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more nucleic acids. Ligation incubation times may be at most 30 seconds, 1 minute, 2 minutes, 5 minutes, 10 minutes, 20 minutes, 30 minutes, 1 hour, or longer. Longer incubation times may improve ligation efficiency.

[0133] Ligation may require nucleic acids with 5' phosphorylated ends. Nucleic acid components without 5' phosphorylated ends may be phosphorylated in a reaction with polynucleotide kinase, such as T4 polynucleotide kinase (or T4 PNK). Other co-factors may be present in the reaction such as ATP, magnesium ion, or DTT. Polynucleotide kinase reactions may occur at 37 degrees Celsius for 30 minutes. Polynucleotide kinase reaction temperatures may be at least 4, 10, 20, 20, 30, 40, 50, or 60 degrees Celsius. Polynucleotide kinase reaction incubation times may be at most, 1 minute, 5 minutes, 10 minutes, 20 minutes, 30 minutes, 60 minutes, or more.

Alternatively, the nucleic acid components may be synthetically (as opposed to enzymatically) designed and manufactured with a modified 5' phosphorylation. Only nucleic acids being assembled on their 5' ends may require phosphorylation. For example, templates in TDL may not be phosphorylated as they are not intended to be assembled.

[0134] Additives may be included in a ligation reaction to improve ligation efficiency. For example, the addition of Dimethyl sulfoxide (DMSO), polyethylene glycol (PEG), 1,2- Propanediol (1,2-Prd), glycerol, Tween-20 or combinations thereof. PEG6000 may be a particularly effective ligation enhancer. PEG6000 may increase ligation efficiency by acting as a crowding agent. For example, the PEG6000 may form aggregated nodules that take up space in the ligase reaction solution and bring the ligase and components to closer proximity. Additive content (weight per volume) may be at least 0%, 1%, 5%, 10%, 20%, or more.

[0135] Various ligases may be used for ligation. The ligases can be naturally occurring or synthesized. Examples of ligases include T4 DNA Ligase, T7 DNA Ligase, T3 DNA Ligase, Taq DNA Ligase, 9oNTM DNA Ligase, E. coli DNA Ligase, and SplintR DNA Ligase. Different ligases may be stable and function optimally at different temperatures. For example, Taq DNA Ligase is thermostable and T4 DNA Ligase is not. Moreover, different ligases have different properties. For example, T4 DNA Ligase may ligate blunt-ended dsDNA while T7 DNA Ligase may not.

[0136] Ligation may be used to attach sequencing adapters to a library of nucleic acids. For example, the ligation may be performed with common sticky ends or staples at the ends of each member of the nucleic acid library. If the sticky end or staple at one end of the nucleic acids is distinct from that of the other end, then the sequencing adapters may be ligated asymmetrically. For example, a forward sequencing adapter may be ligated to one end of the members of the nucleic acid library and a reverse sequencing adapter may be ligate to the other end of the members of the nucleic acid library. Alternatively, blunt-ended ligation may be used to attach adapters to a library of blunt-ended double-stranded nucleic acids. Fork adapters may be used to asymmetrically attach adapters to a nucleic acid library with either blunt ends or sticky ends that are equivalent at each end (such as A-tails).

[0137] Ligation may be inhibited by heat inactivation (for example incubation at 65 degrees Celsius for at least 20 minutes), addition of a denaturant, or addition of a chelator such as EDTA.

C. Restriction digest

[0138] Restriction digests are reactions in which restriction endonucleases (or restriction enzymes) recognize their cognate restriction site on nucleic acids and subsequently cleave (or digest) the nucleic acids containing said restriction site. Type I, type II, type III, or type IV restriction enzymes may be used for restriction digests. Type II restriction enzymes may be the most efficient restriction enzymes for nucleic acid digestions. Type II restriction enzymes may recognize palindromic restriction sites and cleave nucleic acids within the recognition site. Examples of said restriction enzymes (and their restriction sites) include Aatll (GACGTC), Afel (AGCGCT), Apal (GGGCCC), Dpnl (GATC), EcoRI (GAATTC), Ngel (GCTAGC), and many more. Some restriction enzymes, such as Dpnl and Afel, may cut their restriction sites in the center, thus leaving blunt-ended dsDNA products. Other restriction enzymes, such as EcoRI and Aatll, cut their restriction sites off-center, thus leaving dsDNA products with sticky ends (or staggered ends). Some restriction enzymes may target discontinuous restriction sites. For example, the restriction enzyme AlwNI recognizes the restriction site CAGNNNCTG, where N may be either A, T, C, or G. Restriction sites may be at least 2, 4, 6, 8, 10, or more bases long. [0139] Some Type II restriction enzymes cleave nucleic acids outside of their restriction sites. The enzymes may be sub-classified as either Type IIS or Type IIG restriction enzymes. Said enzymes may recognize restriction sites that are non-palindromic. Examples of said restriction enzymes include BbsI, that recognizes GAAAC and creates a staggered cleavage 2 (same strand) and 6 (opposite strand) bases further downstream. Another example includes Bsal, that recognizes GGTCTC and creates a staggered cleavage 1 (same strand) and 5 (opposite strand) bases further downstream. Said restriction enzymes may be used for golden gate assembly or modular cloning (MoClo). Some restriction enzymes, such as Bcgl (a Type IIG restriction enzyme) may create a staggered cleavage on both ends of its recognition site. Restriction enzymes may cleave nucleic acids at least 1, 5, 10, 15, 20, or more bases away from their recognition sites. Because said restriction enzymes may create staggered cleavages outside of their recognitions sites, the sequences of the resulting nucleic acid overhangs may be arbitrarily designed. This is as opposed to restriction enzymes that create staggered cleavages within their recognition sites, where the sequence of a resulting nucleic acid overhang is coupled to the sequence of the restriction site. Nucleic acid overhangs created by restriction digests may be at least 1, 2, 3, 4, 5, 6, 7, 8, or more bases long. When restriction enzymes cleave nucleic acids, the resulting 5' ends contain a phosphate.

[0140] One or more nucleic acid sequences may be included in a restriction digest reaction. Likewise, one or more restriction enzymes may be used together in a restriction digest reaction. Restriction digests may contain additives and cofactors including potassium ion, magnesium ion, sodium ion, BSA, S-Adenosyl-L-methionine (SAM), or combinations thereof. Restriction digest reactions may be incubated at 37 degrees Celsius for one hour. Restriction digest reactions may be incubated in temperatures of at least 0, 10, 20, 30, 40, 50, or 60 degrees Celsius. Optimal digest temperatures may depend on the enzymes. Restriction digest reactions may be incubated for at most 1, 10, 30, 60, 90, 120, or more minutes. Longer incubation times may result in increased digestion.

D. Nucleic acid amplification

[0141] Nucleic acid amplification may be executed with polymerase chain reaction, or PCR. In PCR, a starting pool of nucleic acids (referred to as the template pool or template) may be combined with polymerase, primers (short nucleic acid probes), nucleotide tri phosphates (such as dATP, dTTP, dCTP, dGTP, and analogs or variants thereof), and additional cofactors and additives such as betaine, DMSO, and magnesium ion. The template may be single stranded or double stranded nucleic acids. The primer may be a short nucleic acid sequence built synthetically to complement and hybridize to a target sequence in the template pool. Typically, there are two primers in a PCR reaction, one to complement a primer binding site on the top strand of a target template, and another to complement a primer binding site on the bottom strand of the target template downstream of the first binding site. The 5'-to-3 ' orientation in which these primers bind their target must be facing each other in order to successfully replicate and exponentially amplify the nucleic acid sequence in between them. Though "PCR" may typically refer to reactions specifically of said form, it may also be used more generally to refer to any nucleic acid amplification reaction.

[0142] In some implementations, PCR may comprise cycling between three temperatures: a melting temperature, an annealing temperature, and an extension temperature. The melting temperature is intended to turn double stranded nucleic acids into single stranded nucleic acids, as well as remove the formation of hybridization products and secondary structures. Typically the melting temperature is high, for example above 95 degrees Celsius. In some implementations the melting temperature may be at least 96, 97, 98, 99, 100, 101, 102, 103, 104, or 105 degrees Celsius. In other implementations the melting temperature may be at most 95, 94, 93, 92, 91, or 90 degrees Celsius. A higher melting temperature will improve dissociation of nucleic acids and their secondary structures, but may also cause side effects such as the degradation of nucleic acids or the polymerase. Melting temperatures may be applied to the reaction for at least 1, 2, 3, 4, 5 seconds, or above, such as 30 seconds, 1 minute, 2 minutes, or 3 minutes. A longer initial melting temperature step may be recommended for PCR with complex or long template.

[0143] The annealing temperature is intended to facilitate the formation of hybridization between the primers and their target templates. In some implementations, the annealing temperature may match the calculated melting temperature of the primer. In other implementations, the annealing temperature may be within 10 degrees Celsius or more of said melting temperature. In some implementations, the annealing temperature may be at least 25, 30, 50, 55, 60, 65, or 70 degrees Celsius. The melting temperature may depend on the sequence of the primer. Longer primers may have higher melting temperatures, and primers with higher percent content of Guanine or Cytosine nucleotides may have higher melting temperatures. It may therefore be possible to design primers intended to assemble optimally at particular annealing temperatures. Annealing temperatures may be applied to the reaction for at least 1, 5, 10, 15, 20, 25, or 30 seconds, or above. To help ensure annealing, the primer concentrations may be at high or saturating amounts. Primer concentrations may be 500 nanomolar (nM). Primer concentrations may be at most InM, 10 nM, 100 nM, 1000 nM, or more.

[0144] The extension temperature is intended to initiate and facilitate the 3' end nucleic acid chain elongation of primers catalyzed by one or more polymerase enzymes. In some implementations, the extension temperature may be set at the temperature in which the polymerase functions optimally in terms of nucleic acid binding strength, elongation speed, elongation stability, or fidelity. In some implementations, the extension temperature may be at least 30, 40, 50, 60, or 70 degrees Celsius, or above. Annealing temperatures may be applied to the reaction for at least 1, 5, 10, 15, 20, 25, 30, 40, 50, or 60 seconds or above. Recommended extension times may be approximately 15 to 45 seconds per kilobase of expected elongation. [0145] In some implementations of PCR, the annealing temperature and the extension temperature may be the same. Thus a 2-step temperature cycle may be used instead of a 3 -step temperature cycle. Examples of combined annealing and extension temperatures include 60, 65, or 72 degrees Celsius.

[0146] In some implementations, PCR may be performed with one temperature cycle. Such implementations may involve turning targeted single stranded template nucleic into double stranded nucleic acid. In other implementations, PCR may be performed with multiple temperature cycles. If the PCR is efficient, it is expected that the number of target nucleic acid molecules will double each cycle, thereby creating an exponential increase in the number of targeted nucleic acid templates from the original template pool. The efficiency of PCR may vary. Therefore, the actual percent of targeted nucleic acid that is replicated each round may be more or less than 100%. Each PCR cycle may introduce undesirable artifacts such as mutated and recombined nucleic acids. To curtail this potential detriment, a polymerase with high fidelity and high processivity may be used. In addition, a limited number of PCR cycles may be used. PCR may involve at most 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, or more cycles.

[0147] In some implementations, multiple distinct target nucleic acid sequences may amplified together in one PCR. If each target sequence has common primer binding sites, then all nucleic acid sequences may be amplified with the same set of primers. Alternatively, PCR may comprise multiple primers intended to each target distinct nucleic acids. Said PCR may be referred to as multiplex PCR. PCR may involve at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more distinct primers. In PCR with multiple distinct nucleic acid targets, each PCR cycle may change the relative distribution of the targeted nucleic acids. For example, a uniform distribution may become skewed or non-uniformly distributed. To curtail this potential detriment, optimal polymerases (e.g., with high fidelity and sequence robustness) and optimal PCR conditions may be used. Factors such as annealing and extension temperature and time may be optimized. In addition, a limited number of PCR cycles may be used.

[0148] In some implementations of PCR, a primer with base mismatches to its targeted primer binding site in the template may be used to mutate the target sequence. In some implementations of PCR, a primer with an extra sequence on its 5' end (known as an overhang) may be used to attach a sequence to its targeted nucleic acid. For example, primers containing sequencing adapters on their 5' ends may be used to prepare and/or amplify a nucleic acid library for sequencing. Primers that target sequencing adapters may be used to amplify nucleic acid libraries to sufficient enrichment for certain sequencing technologies. [0149] In some implementations, linear-PCR (or asymmetric-PCR) is used wherein primers only target one strand (not both strands) of a template. In linear-PCR the replicated nucleic acid from each cycle is not complemented to the primers, so the primers do not bind it. Therefore, the primers only replicate the original target template with each cycle, hence the linear (as opposed to exponential) amplification. Though the amplification from linear-PCR may not be as fast as conventional (exponential) PCR, the maximal yield may be greater. Theoretically, the primer concentration in linear-PCR may not become a limiting factor with increased cycles and increased yield as it would with conventional PCR. Linear- After- The-Exponential-PCR (or LATE-PCR) is a modified version of linear-PCR that may be capable of particularly high yields. [0150] In some implementations of nucleic acid amplification, the process of melting, annealing, and extension may occur at a single temperature. Such PCR may be referred to as isothermal PCR. Isothermal PCR may leverage temperature-independent methods for dissociating or displacing the fully-complemented strands of nucleic acids from each other in favor of primer binding. Strategies include loop-mediated isothermal amplification, strand displacement amplification, helicase-dependent amplification, and nicking enzyme amplification reaction. Isothermal nucleic acid amplification may occur at temperatures of at most 20, 30, 40, 50, 60, or 70 degrees Celsius or more.

[0151] In some implementations, PCR may further comprise a fluorescent probe or dye to quantify the amount of nucleic acid in a sample. For example, the dye may interpolate into double stranded nucleic acids. An example of said dye is SYBR Green. A fluorescent probe may also be a nucleic acid sequence attached to a fluorescent unit. The fluorescent unit may be release upon hybridization of the probe to a target nucleic acid and subsequent modification from an extending polymerase unit. Examples of said probes include Taqman probes. Such probes may be used in conjunction with PCR and optical measurement tools (for excitation and detection) to quantify nucleic acid concentration in a sample. This process may be referred to as quantitative PCR (qPCR) or real-time PCR (rtPCR). [0152] In some implementations, a PCR may be performed on single a molecule template (in a process that may be referred to as single-molecule PCR), rather than on a pool of multiple template molecules. For example, emulsion-PCR (ePCR) may be used to encapsulate single nucleic acid molecules within water droplets within an oil emulsion. The water droplets may also contain PCR reagents, and the water droplets may be held in a temperature-controlled environment capable of requisite temperature cycling for PCR. This way, multiple self-contained PCR reactions may occur simultaneously in high throughput. The stability of oil emulsions may be improved with surfactants. The movement of droplets may be controlled with pressure through microfluidic channels. Microfluidic devices may be used to create droplets, split droplets, merge droplets, inject material intro droplets, and to incubate droplets. The size of water droplets in oil emulsions may be at least 1 picoliter (pL), 10 pL, 100 pL, 1 nanoliter (nL), 10 nL, 100 nL, or more.

[0153] In some implementations, single-molecule PCR may be performed on a solid-phase substrate. Examples include the Illumina solid-phase amplification method or variants thereof. The template pool may be exposed to a solid-phase substrate, wherein the solid phase substrate may immobilize templates at a certain spatial resolution. Bridge amplification may then occur within the spatial neighborhood of each template thereby amplifying single molecules in a high throughput fashion on the substrate.

[0154] High-throughput, single-molecule PCR may be useful for amplifying a pool of distinct nucleic acids that may interfere with each other. For example, if multiple distinct nucleic acids share a common sequence region, then recombination between the nucleic acids along this common region may occur during the PCR reaction, resulting in new, recombined nucleic acids. Single-molecule PCR would prevent this potential amplification error as it compartmentalizes distinct nucleic acid sequences from each other so they may not interact. Single-molecule PCR may be particularly useful for preparing nucleic acids for sequencing. Single-molecule PCR mat also be useful for absolute quantitation of a number of targets within a template pool. For example, digital PCR (or dPCR), uses the frequency of distinct single-molecule PCR amplification signals to estimate the number of starting nucleic acid molecules in a sample. [0155] In some implementations of PCR, a group of nucleic acids may be non-discriminantly amplified using primers for primer binding sites common to all nucleic acids. For example, primers for primer binding sites flanking all nucleic acids in a pool. Synthetic nucleic acid libraries may be created or assembled with these common sites for general amplification. However, in some implementations, PCR may be used to selectively amplify a targeted subset of nucleic acids from a pool. For example, by using primers with primer binding sites that only appear on said targeted subset of nucleic acids. Synthetic nucleic acid libraries may be created or assembled such that nucleic acids belonging to potential sub-libraries of interest all share common primer binding sites on their edges (common within the sub-library but distinct from other sub-libraries) for selective amplification of the sub-library from the more general library. In some implementations, PCR may be combined with nucleic acid assembly reactions (such as ligation or OEPCR) to selectively amplify fully assembled or potentially fully assembled nucleic acids from partially assembled or mis-assembled (or unintended or undesirable) bi-products. For example, the assembly may involve assembling a nucleic acid with a primer binding site on each edge sequence such that only a full assembled nucleic product would contain the requisite two primer binding sites for amplification. In said example, a partially assembled product may contain neither or only one of the edge sequences with the primer binding sites, and therefore should not be amplified. Likewise a mis-assembled (or unintended or undesirable) product may contain neither or only one of the edge sequences, or both edge sequences but in the incorrect orientation or separated by an incorrect amount of bases. Therefore said mis-assembled product should either not amplify or amplify to create a product of incorrect length. In the latter case the amplified mis-assembled product of incorrect length may be separated from the amplified fully assembled product of correct length by nucleic acid size selection methods, such as DNA electrophoresis in an agarose gel followed by gel extraction. [0156] Additives may be included in the PCR to improve the efficiency of nucleic acid amplification. For example, the addition of Betaine, Dimethyl sulfoxide (DMSO), non-ionic detergents, Formamide, Magnesium, Bovine Serum Albumin (BSA), or combinations thereof. Additive content (weight per volume) may be at least 0%, 1%, 5%, 10%, 20%, or more.

[0157] Various polymerases may be used for PCR. The polymerase can be naturally occurring or synthesized. An example polymerase is a 29 polymerase or derivative thereof. In some cases, a transcriptase or a ligase is used (i.e., enzymes which catalyze the formation of a bond) in conjunction with polymerases or as an alternative to polymerases to construct new nucleic acid sequences. Examples of polymerases include a DNA polymerase, a RNA polymerase, a thermostable polymerase, a wild-type polymerase, a modified polymerase, E. coli DNA polymerase I, T7 DNA polymerase, bacteriophage T4 DNA polymerase 029 (phi29) DNA polymerase, Taq polymerase, Tth polymerase, Tli polymerase, Pfu polymerase Pwo polymerase, VENT polymerase, DEEPVENT polymerase, Ex-Taq polymerase, LA-Taw polymerase, Sso polymerase Poc polymerase, Pab polymerase, Mth polymerase ES4 polymerase, Tru polymerase, Tac polymerase, Tne polymerase, Tma polymerase, Tea polymerase, Tih polymerase, Tfi polymerase, Platinum Taq polymerases, Tbr polymerase, Phusion polymerase, KAPA polymerase, Q5 polymerase, Tfl polymerase, Pfutubo polymerase, Pyrobest polymerase, KOD polymerase, Bst polymerase, Sac polymerase, KI enow fragment polymerase with 3’ to 5’ exonuclease activity, and variants, modified products and derivatives thereof. Different polymerases may be stable and function optimally at different temperatures. Moreover, different polymerases have different properties. For example, some polymerases, such a Phusion polymerase, may exhibit 3' to 5' exonuclease activity, which may contribute to higher fidelity during nucleic acid elongation. Some polymerases may displace leading sequences during elongation, while others may degrade them or halt elongation. Some polymerases, like Taq, incorporate an adenine base at the 3' end of nucleic acid sequences. Additionally, some polymerases may have higher fidelity and processivity than others and may be more suitable to PCR applications, such as sequencing preparation, where it is important for the amplified nucleic acid yield to have minimal mutations and where it is important for the distribution of distinct nucleic acids to maintain uniform distribution throughout amplification.

E. Size selection

[0158] Nucleic acids of a particular size may be selected from a sample using size-selection techniques. In some implementations, size-selection may be performed using gel electrophoresis or chromatography. Liquid samples of nucleic acids may be loaded onto one terminal of a stationary phase or gel (or matrix). A voltage difference may be placed across the gel such that the negative terminal of the gel is the terminal at which the nucleic acid samples are loaded and the positive terminal of the gel is the opposite terminal. Since the nucleic acids have a negatively charged phosphate backbone, they will migrate across the gel to the positive terminal. The size of the nucleic acid will determine its relative speed of migration through the gel. Therefore nucleic acids of different sizes will resolve on the gel as they migrate. Voltage differences may be 100V or 120V. Voltage differences may be at most 50V, 100V, 150V, 200V, 250V, or more. Larger voltage differences may increase the speed of nucleic acid migration and size resolution.

However, larger voltage differences may also damage the nucleic acids or the gel. Larger voltage differences may be recommended for resolving nucleic acids of larger sizes. Typical migration times may be between 15 minutes and 60 minutes. Migration times may be at most 10 minutes, 30 minutes, 60 minutes, 90 minutes, 120 minutes, or more. Longer migration times, similar to higher voltage, may lead to better nucleic acid resolution but may lead to increased nucleic acid damage. Longer migration times may be recommended for resolving nucleic acids of larger sizes. For example, a voltage difference of 120V and a migration time of 30 minutes may be sufficient for resolving a 200-base nucleic acid from a 250-base nucleic acid.

[0159] The properties of the gel, or matrix, may affect the size-selection process. Gels typically comprise a polymer substance, such as agarose or polyacrylamide, dispersed in a conductive buffer such as TAE (Tris-acetate-EDTA) or TBE (Tris-borate-EDTA). The content (weight per volume) of the substance (e.g. agarose or acrylamide) in the gel may be at most .5%, 1%, 2%, 3%, 5%, 10%, 15%, 20%, 25%, or higher. Higher content may decrease migration speed. Higher content may be preferable for resolving smaller nucleic acids. Agarose gels may be better for resolving double stranded DNA (dsDNA). Polyacrylamide gels may be better for resolving single stranded DNA (ssDNA). The preferred gel composition may depend on the nucleic acid type and size, the compatibility of additives (e.g., dyes, stains, denaturing solutions, or loading buffers) as well as the anticipate downstream applications (e.g., gel extraction then ligation, PCR, or sequencing). Agarose gels may be simpler for gel extraction than polyacrylamide gels. TAE, though not as good a conductor as TBE, may also be better for gel extraction because borate (an enzyme inhibitor) carry-over in the extraction process may inhibit downstream enzymatic reactions.

[0160] Gels may further comprise a denaturing solution such as SDS (sodium dodecyl sulfate) or urea. SDS may be used, for example, to denature proteins or to separate nucleic acids from potentially bound proteins. Urea may be used to denature secondary structures in DNA. For example, urea may convert dsDNA into ssDNA, or urea may convert a folded ssDNA (for example a hairpin) to a non-folded ssDNA. Urea-polyacrylamide gels (further comprising TBE) may be used for accurately resolving ssDNA.

[0161] Samples may be incorporate into gels with different formats. In some implementations, gels may contain wells in which samples may be loaded manually. One gel may have multiple wells for running multiple nucleic acids samples. In other implementations, the gels may be attached to microfluidic channels that automatically load the nucleic acid sample(s). Each gel may be downstream of several microfluidic channels, or the gels themselves may each occupy separate microfluidic channels. The dimensions of the gel may affect the sensitivity of nucleic acid detection (or visualization). For example, thin gels or gels inside of microfluidic channels (such as in bioanalyzers or tapestations) may improve the sensitivity of nucleic acid detection. The nucleic acid detection step may be important for selecting and extracting a nucleic acid fragment of the correct size.

[0162] A ladder may be loaded into a gel for nucleic acid size reference. The ladder may contain markers of different sizes to which the nucleic acid sample may be compared. Different ladders may have different size ranges and resolutions. For example a 50 base ladder may have markers at 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, and 600 bases. Said ladder may be useful for detecting and selecting nucleic acids within the size range of 50 and 600 bases. The ladder may also be used as a standard for estimating the concentration of nucleic acids of different sizes in a sample.

[0163] Nucleic acid samples and ladders may be mixed with loading buffer to facilitate the gel electrophoresis (or chromatography) process. Loading buffer may contain dyes and markers to help track the migration of the nucleic acids. Loading buffer may further comprise reagents (such as glycerol) that are denser than the running buffer (e.g., TAE or TBE), to ensure that nucleic acid samples sink to the bottom of the sample loading wells (which may be submerged in the running buffer). Loading buffer may further comprise denaturing agents such as SDS or urea. Loading buffer may further comprise reagents for improving the stability of nucleic acids. For example, loading buffer may contain EDTA to protect nucleic acids from nucleases.

[0164] In some implementations, the gel may comprise a stain that binds the nucleic acid and that may be used to optically detect nucleic acids of different sizes. Stains may be specific for dsDNA, ssDNA, or both. Different stains may be compatible with different gel substances. Some stains may require excitation from a source light (or electromagnetic wave) in order to visualize. The source light may be UV (ultraviolet) or blue light. In some implementations, stains may be added to the gel prior to electrophoresis. In other implementations, stains may be added to the gel after electrophoresis. Examples of stains include Ethidium Bromide (EtBr), SYBR Safe, SYBR Gold, silver stain, or methylene blue. A reliable method for visualizing dsDNA of a certain size, for example, may be to use an agarose TAE gel with a SYBR Safe or EtBr stain. A reliable method for visualizing ssDNA of a certain size, for example, may be to use a ureapolyacrylamide TBE gel with a methylene blue or silver stain.

[0165] In some implementations, the migration of nucleic acids through gels may be driven by other methods besides electrophoresis. For example, gravity, centrifugation, vacuums, or pressure may be used to drive nucleic acids through gels so that they may resolve according to their size.

[0166] Nucleic acids of a certain size may be extracted from gels using a blade or razor to excise the band of gel containing the nucleic acid. Proper optical detection techniques and DNA ladders may be used to ensure that the excision occurs precisely at a certain band and that the excision successfully excludes nucleic acids that may belong to different, undesirable size bands. The gel band may be incubated with buffer to dissolve it, thus releasing the nucleic acids into the buffer solution. Heat or physical agitation may speed the dissolution. Alternatively, the gel band may be incubated in buffer long enough to allow diffusion of the DNA into the buffer solution without requiring gel dissolution. The buffer may then be separated from the remaining solid-phase gel, for example by aspiration or centrifugation. The nucleic acids may then be purified from the solution using standard purification or buffer-exchange techniques, such as phenol-chloroform extraction, ethanol precipitation, magnetic bead capture, and/or silica membrane adsorption, washing, and elution. Nucleic acids may also be concentrated in this step.

[0167] As an alternative to gel excision, nucleic acids of a certain size may be separated from a gel by allowing them to run off the gel. Migrating nucleic acids may pass through a basin (or well) either embedded in the gel or at the end of the gel. The migration process may be timed or optically monitored such that when the nucleic acid group of a certain size enters the basin, the sample is collected from the basin. The collection may occur, for example, by aspiration. The nucleic acids may then be purified from the collected solution using standard purification or buffer-exchange techniques, such as phenol-chloroform extraction, ethanol precipitation, magnetic bead capture, and/or silica membrane adsorption, washing, and elution. Nucleic acids may also be concentrated in this step.

[0168] Other methods for nucleic acid size selection may include mass-spectrometry or membrane-based filtration. In some implementations of membrane-based filtration, nucleic acids are passed through a membrane (for example a silica membrane) that may preferentially bind to either dsDNA, ssDNA, or both. The membrane may be designed to preferentially capture nucleic acids of at least a certain size. For example, membranes may be designed to filter out nucleic acids of less than 20, 30, 40, 50, 70, 90, or more bases. Said membrane-based, sizeselection techniques may not be as stringent as gel electrophoresis or chromatography, F. Nucleic acid capture

[0169] Affinity-tagged nucleic acids may be used as sequence specific probes for nucleic acid capture. The probe may be designed to complement a target sequence within a pool of nucleic acids. Subsequently, the probe may be incubated with the nucleic acid pool and hybridized to its target. The incubation temperature may be below the melting temperature of the probe to facilitate hybridization. The incubation temperature may be up to 5, 10, 15, 20, 25, or more degrees Celsius below the melting temperature of the probe. The hybridized target may be captured to a solid-phase substrate that specifically binds the affinity tag. The solid-phase substrate may be a membrane, a well, a column, or a bead. Multiple rounds of washing may remove all non-hybridized nucleic acids from the targets. The washing may occur at a temperature below the melting temperature of the probe to facilitate stable immobilization of target sequences during the wash. The washing temperature may be up to 5, 10, 15, 20, 25, or more degrees Celsius below the melting temperature of the probe. A final elution step may recover the nucleic acid targets from the solid phase- substrate, as well as from the affinity tagged probes. The elution step may occur at a temperature above the melting temperature of the probe to facilitate the release of nucleic acid targets into an elution buffer. The elution temperature may be up to 5, 10, 15, 20, 25, or more degrees Celsius above the melting temperature of the probe.

[0170] In certain implementations, the oligonucleotides bound to a solid-phase substrate may be removed from the solid-phase substrate, for example, by exposure to conditions such as acid, base, oxidation, reduction, heat, light, metal ion catalysis, displacement or elimination chemistry, or by enzymatic cleavage. In certain embodiments, the oligonucleotides may be attached to a solid support through a cleavable linkage moiety. For example, the solid support may be functionalized to provide cleavable linkers for covalent attachment to the targeted oligonucleotides. In some embodiments, the linker moiety may be of six or more atoms in length. In some embodiments, the cleavable linker may be a TOPS (two oligonucleotides per synthesis) linker, an amino linker, or a photocleavable linker.

[0171] In some implementations, biotin may be used as an affinity tag that is immobilized by streptavidin on a solid-phase substrate. Biotinylated oligonucleotides, for use as nucleic acid capture probes, may be designed and manufactured. Oligonucleotides may be biotinylated on the 5' or 3' end. They may also be biotinylated internally on thymine residues. Increased biotin on an oligo may lead to stronger capture on the streptavidin substrate. A biotin on the 3' end of an oligo may block the oligo from extending during PCR. The biotin tag may be a variant of standard biotin. For example, the biotin variant may be biotin-TEG (tri ethylene glycol), dual biotin, PC biotin, DesthioBiotin-TEG, and biotin Azide. Dual biotin may increase the biotin-streptavidin affinity. Biotin-TEG attaches the biotin group onto a nucleic acid separated by a TEG linker. This may prevent the biotin from interfering with the function of the nucleic acid probe, for example its hybridization to the target. A nucleic acid biotin linker may also be attached to the probe. The nucleic acid linker may comprise nucleic acid sequences that are not intended to hybridize to the target.

[0172] The biotinylated nucleic acid probe may be designed with consideration for how well it may hybridize to its target. Nucleic acid probes with higher designed melting temperatures may hybridize to their targets more strongly. Longer nucleic acid probes, as well as probes with higher GC content, may hybridize more strongly due to increased melting temperatures. Nucleic acid probes may have a length of a least 5, 10, 15, 20, 30, 40, 50, or 100 bases, or more. Nucleic acid probes may have a GC content anywhere between 0 and 100%. Care may be taken to ensure that the melting temperature of the probe does not exceed the temperature tolerance of the streptavidin substrate. Nucleic acid probes may be designed to avoid inhibitory secondary structures such as hairpins, homodimers, and heterodimers with off-target nucleic acids. There may be a tradeoff between probe melting temperature and off-target binding. There may be an optimal probe length and GC content at which melting temperature is high and off-target binding is low. A synthetic nucleic acid library may be designed such that its nucleic acids comprise efficient probe binding sites.

[0173] The solid-phase streptavidin substrate may be magnetic beads. Magnetic beads may be immobilized using a magnetic strip or plate. The magnetic strip or plate may be brought into contact with a container to immobilize the magnetic beads to the container. Conversely, the magnetic strip or plate may be removed from a container to release the magnetic beads from the container wall into a solution. Different bead properties may affect their application. Beads may have varying sizes. For example beads may be anywhere between 1 and 3 micrometers (um) in diameter. Beads may have a diameter of at most 1, 2, 3, 4, 5, 10, 15, 20, or more micrometers. Bead surfaces may be hydrophobic or hydrophilic. Beads may be coated with blocking proteins, for example BSA. Prior to use, beads may be washed or pre-treated with additives, such as blocking solution to prevent them from non-specifically binding nucleic acids.

[0174] A biotinylated probe may be coupled to the magnetic streptavidin beads prior to incubation with the nucleic acid sample pool. This process may be referred to as direct capture. Alternatively, the biotinylated probe may be incubated with the nucleic acid sample pool prior to the addition of magnetic streptavidin beads. This process may be referred to as indirect capture. The indirect capture method may improve target yield. Shorter nucleic acid probes may require a shorter amount of time to couple to the magnetic beads.

[0175] Optimal incubation of the nucleic acid probe with the nucleic acid sample may occur at a temperature that is 1 to 10 degrees Celsius or more below the melting temperature of the probe. Incubation temperatures may be at most 5, 10, 20, 30, 40, 50, 60, 70, 80, or more degrees Celsius. The recommended incubation time may be 1 hour. The incubation time may be at most 1, 5, 10, 20, 30, 60, 90, 120, or more minutes. Longer incubation times may lead to better capture efficiency. An additional 10 minutes of incubation may occur after the addition of the streptavidin beads to allow biotin-streptavidin coupling. This additional time may be at most 1, 5, 10, 20, 30, 60, 90, 120, or more minutes. Incubation may occur in buffered solution with additives such as sodium ion.

[0176] Hybridization of the probe to its target may be improved if the nucleic acid pool is singlestranded nucleic acid (as opposed to double-stranded). Preparing a ssDNA pool from a dsDNA pool may entail performing linear-PCR with one primer that commonly binds the edge of all nucleic acid sequences in the pool. If the nucleic acid pool is synthetically created or assembled, then this common primer binding site may be included in the synthetic design. The product of the linear-PCR will be ssDNA. More starting ssDNA template for the nucleic acid capture may be generated with more cycles of linear-PCR.

[0177] After the nucleic acid probes are hybridized to their targets and coupled to magnetic streptavidin beads, the beads may be immobilized by a magnet and several rounds of washing may occur. Three to five washes may be sufficient to remove non-target nucleic acids, but more or less rounds of washing may be used. Each incremental wash may further decrease nontargeted nucleic acids, but it may also decrease the yield of target nucleic acids. To facilitate proper hybridization of the target nucleic acids to the probe during the wash step, a low incubation temperature may be used. Temperatures as low as 60, 50, 40, 30, 20, 10, or 5 degrees Celsius or less may be used. The washing buffer may comprise Tris buffered solution with sodium ion.

[0178] Optimal elution of the hybridized targets from the magnetic bead-coupled probes may occur at a temperature that is equivalent to or more than the melting temperature of the probe. Higher temperatures will facilitate the dissociation of the target to the probe. Elution temperatures may be at most 30, 40, 50, 60, 70, 80, or 90 degrees Celsius, or more. Elution incubation time may be at most 1, 2, 5, 10, 30, 60 or more minutes. Typical incubation times may be approximately 5 minutes, but longer incubation times may improve yield. Elution buffer may be water or tris-buffered solution with additives such as EDTA.

[0179] Nucleic acid capture of target sequences containing at least one or more of a set of distinct sites may be performed in one reaction with multiple distinct probes for each of those sites. Nucleic acid capture of target sequences containing every member of a set of distinct sites may be performed in a series of capture reactions, one reaction for each distinct site using a probe for that particular site. The target yield after a series of capture reactions may be low, but the captured targets may subsequently be amplified with PCR. If the nucleic acid library is synthetically designed, then the targets may be designed with common primer binding sites for PCR.

[0180] Synthetic nucleic acid libraries may be created or assembled with common probe binding sites for general nucleic acid capture. These common sites may be used to selectively capture fully assembled or potentially fully assembled nucleic acids from assembly reactions, thereby filtering out partially assembled or mis-assembled (or unintended or undesirable) bi-products. For example, the assembly may involve assembling a nucleic acid with a probe binding site on each edge sequence such that only a fully assembled nucleic product would contain the requisite two probe binding sites necessary to pass through a series of two capture reactions using each probe. In said example, a partially assembled product may contain neither or only one of the probe sites, and therefore should not ultimately be captured. Likewise a mis-assembled (or unintended or undesirable) product may contain neither or only one of the edge sequences. Therefore said misassembled product may not ultimately be captured. For increased stringency, common probe binding sites may be included on each component of an assembly. A subsequent series of nucleic acid capture reactions using a probe for each component may isolate only fully assembled product (containing each component) from any bi-products of the assembly reaction. Subsequent PCR may improve target enrichment, and subsequent size-selection may improve target stringency.

[0181] In some implementations, nucleic acid capture may be used to selectively capture a targeted subset of nucleic acids from a pool. For example, by using probes with binding sites that only appear on said targeted subset of nucleic acids. Synthetic nucleic acid libraries may be created or assembled such that nucleic acids belonging to potential sub-libraries of interest all share common probe binding sites (common within the sub-library but distinct from other sublibraries) for the selective capture of the sub-library from the more general library.

G. Lyophilization

[0182] Lyophilization is a dehydration process. Both nucleic acids and enzymes may be lyophilized. Lyophilized substances may have longer lifetimes. Additives such as chemical stabilizers may be used to maintain functional products (e.g., active enzymes) through the lyophilization process. Disaccharides, such as sucrose and trehalose, may be used as chemical stabilizers.

H. DNA design

[0183] The sequences of nucleic acids (e.g., components) for building synthetic libraries (e.g., identifier libraries) may be designed to avoid synthesis, sequencing, and assembly complications. Moreover, they may be designed to decrease the cost of building the synthetic library and to improve the lifetime over which the synthetic library may be stored.

[0184] Nucleic acids may be designed to avoid long strings of homopolymers (or repeated base sequences) that may be difficult to synthesize. Nucleic acids may be designed to avoid homopolymers of length greater than 2, 3, 4, 5, 6, 7 or more. Moreover, nucleic acids may be designed to avoid the formation of secondary structures, such as hairpin loops, that may inhibit their synthesis process. For example, predictive software may be used to generate nucleic acid sequences that do not form stable secondary structures. Nucleic acids for building synthetic libraries may be designed to be short. Longer nucleic acids may be more difficult and expensive to synthesize. Longer nucleic acids may also have a higher chance of mutations during synthesis. Nucleic acids (e.g., components) may be at most 5, 10, 15, 20, 25, 30, 40, 50, 60 or more bases. [0185] Nucleic acids to become components in an assembly reaction may be designed to facilitate that assembly reaction. Efficient assembly reactions typically involve hybridization between adjacent components. Sequences may be designed to promote these on-target hybridization events while avoiding potential off-target hybridizations. Nucleic acid base modifications, such as locked nucleic acids (LNAs), may be used to strengthen on-target hybridization. These modified nucleic acids may be used, for example, as staples in staple strand ligation or as sticky ends in sticky-strand ligation. Other modified bases that may be used for building synthetic nucleic acid libraries (or identifier libraries) include 2,6-Diaminopurine, 5- Bromo dU, deoxyUridine, inverted dT, inverted diDeoxy-T, Dideoxy-C, 5-Methyl dC, deoxyinosine, Super T, Super G, or 5-Nitroindole. Nucleic acids may contain one or multiple of the same or different modified bases. Some of the said modified bases are natural base analogs (for example, 5-Methyl dC and 2,6-Diaminopurine) that have higher melting temperatures and may therefore be useful for facilitating specific hybridization events in assembly reactions. Some of the said modified bases are universal bases (for example, 5-Nitroindole) that can bind to all natural bases and may therefore be useful for facilitating hybridization with nucleic acids that may have variable sequences within desirable binding sites. In addition to their beneficial roles in assembly reactions, these modified bases may be useful in primers (e.g., for PCR) and probes (e.g., for nucleic acid capture) as they may facilitate the specific binding of primers and probes to their target nucleic acids within a pool of nucleic acids. [0186] Nucleic acids may be designed to facilitate sequencing. For example, nucleic acids may be designed to avoid typical sequencing complications such as secondary structure, stretches of homopolymers, repetitive sequences, and sequences with too high or too low of a GC content. Certain sequencers or sequencing methods may be error prone. Nucleic acid sequences (or components) that make up synthetic libraries (e.g., identifier libraries) may be designed with certain hamming distances from each other. This way, even when base resolution errors occur at a high rate in sequencing, the stretches of error-containing sequences may still be mapped back to their most likely nucleic acid (or component). Nucleic acid sequences may be designed with hamming distances of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more base mutations. Alternative distance metrics from hamming distance may also be used to define a minimum requisite distance between designed nucleic acids.

[0187] Some sequencing methods and instruments may require input nucleic acids to contain particular sequences, such as adapter sequences or primer-binding sites. These sequences may be referred to as "method-specific sequences". Typical preparatory workflows for said sequencing instruments and methods may involve assembling the method-specific sequences to the nucleic acid libraries. However, if it is known ahead of time that a synthetic nucleic acid library (e.g., identifier library) will be sequenced with a particular instrument or method, then these methodspecific sequences may be designed into the nucleic acids (e.g., components) that comprise the library (e.g., identifier library). For example, sequencing adapters may be assembled onto the members of a synthetic nucleic acid library in the same reaction step as when the members of a synthetic nucleic acid library are themselves assembled from individual nucleic acid components. [0188] Nucleic acids may be designed to avoid sequences that may facilitate DNA damage. For example, sequences containing sites for site-specific nucleases may be avoided. As another example, UVB (ultraviol et-B) light may cause adjacent thymines to form pyrimidine dimers which may then inhibit sequencing and PCR. Therefore, if a synthetic nucleic acid library is intended to be stored in an environment exposed to UVB, then it may be beneficial to design its nucleic acid sequences to avoid adjacent thymines (i.e., TT).

System for building identifier library

[0189] As described previously, a print-based system, known as the Printer-Finisher System (or PFS), may be used to collocate and assemble components for construction of identifiers.

[0190] Provided herein are systems for assembling an identifier from one or more components for storing information, comprising: (a) a printer for dispensing one or more components onto a substrate, wherein each of the one or more components comprises a nucleic acid sequence; and (b) a finisher for assembling said one or more components on said substrate, wherein said finisher provides a reaction mixture and/or a condition necessary for physically linking one or more nucleic acid sequences.

[0191] In some implementations, said printer further comprises a plurality of printheads, wherein each printhead of said plurality comprises one or more components. In some implementations, said printer comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more printheads. In some implementations, each printhead of said plurality comprises a different component. In some implementations, each printhead comprises at least one nozzle. In some implementations, each printhead comprises a row of nozzles. In some embodiments, each printhead comprises at least 1, 2, 3, 4, or more rows of nozzles. In some implementations, a printhead may be considered a set of nozzles each dispensing the same ink. In some embodiments, the row of nozzles dispenses the same ink. In some implementations, a particular subset of nozzles in a row of nozzles dispense different ink from the other nozzles in said row of nozzles. In some implementations, the row of nozzles comprises at least 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, or more nozzles. In some embodiments, some or all of the nozzles in a row of nozzles may be disjoint. In some implementations, said printhead dispenses a droplet comprising said component onto said substrate. In some implementations, said printhead dispenses a droplet comprises a reaction mix onto said substrate. In some implementations, said droplet is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 picoliter in volume. In some implementations, said droplet is at least 10, 20, 30, 40, 50, 60, 70, or 80 picoliter in volume. In some implementations, said printer further comprises a printer base. In some implementations, said printer further comprises a register, a spot imager, and/or a spot dryer. In some implementations, said one or more components is in solution. In some implementations, said one or more components is a dry component. In some implementations, said reaction mixture comprises a ligase. The ligase can be used to ligate different components comprising nucleic acid sequences. In some implementations, said condition is a temperature condition. In some implementations, said substrate is passed through said printer and/or said finisher with linear movement. In some implementations, said linear movement is controlled by a reel-to-reel system. In some implementations, said spot imager is a camera. In some implementations, said one or more component further comprises a dye. In some implementations, said reaction mix comprises a dye. The dye can be any nucleic acid dye. The dye can be a visible dye.

[0192] In some implementations, said substrate further comprises a polymeric material. In some implementations, said printhead is a MEMS (micro-electro-mechanical systems) thin film piezo inkjet head or a MEMS thermal inkjet head. In some implementations, said one or more components comprises an additive. In some implementations, additive provides compatibility of said one or more component with said printhead. In some implementations, additive is a solute, a humectant, or a surfactant. In some implementations, said spot imager uses a line scan inspection principle. In some implementations, said finisher further comprises a finisher base.

[0193] In some implementations, said finisher further comprises a spot humidifier, a spot imager, and/or a pooling sub-system. In some implementations, said finisher further comprises a printhead. In some implementations, printhead of said finisher dispenses a volume having at least 1 pL, 5 pL, 10 pL, 50 pL, 100 pL, or 200 pL. In some implementations, said finisher comprises a fixed internal temperature that is optimal for reaction incubation. In some implementations, said finisher comprises a loop of rollers. Printer Base System

[0194] The PFS may involve the use of one or more printheads, each capable of printing one or more nucleic acid molecules onto a substrate. Given an identifier library to be generated, the task of assembling all the identifiers that encode a given bitstream may be divided into subtasks where each subtask comprises generating a portion of the identifier library. This portion can be called a "sector" of the identifier library. The size of the sector may be chosen such that any errors in the generation of a sector by the PFS may be detected or corrected by the PFS. Errors may be caused by several sources including but not limited to a malfunctioning printhead, unintended mixing of components during or after printing, variation in the volume of reagents or nucleic acids dispensed by a printhead, misalignment between a printhead and the target coordinate (or spot) on the substrate, or drying or wetting due to high or low humidity. Some of these causes may lead to errors in which one or more identifiers to be generated are not generated. This type of error can be called a missing identifier error.

[0195] Depending on the cause, some missing identifier errors may be detected by the PFS. For example, the PFS may automatically inspect all or a portion of a printed sector using one or more cameras. The PFS may continually or at programmable intervals capture one or more images of each printed sector and subject those images to computational processing to detect whether each reaction specified has been printed on the substrate. In another embodiment, the PFS may continually or at programmable intervals monitor one or more nozzles on one or more printheads and capture images or video of the nozzles as they print a reaction to the substrate. The PFS may subject the video or images captured to image processing to detect whether all intended reagents and nucleic acid droplets were delivered to a reaction. The monitoring cameras may use visible light or light in other frequency bands. In another embodiment, the PFS may periodically print one or more test patterns from all nozzles on all printheads in a test area of the substrate. The PFS may visually capture or analyze the result of the test pattern printing with a spot imager or a camera or some other device with output amenable to analysis. In another embodiment, the PFS may print a test pattern and analyze it using one or more chemical methods of verification such as gel electrophoresis, for example.

[0196] After visual analysis, if the PFS concludes that some or all the components needed to assemble all the specified identifiers were not printed into reactions, then the PFS may report this conclusion to an error log. The control software controlling the PFS may analyze this log, either continually during printing or later, and choose to re-print sectors that contained such missing identifier errors. From the log, the control software may identify malfunctioning printheads or nozzles and print the remaining sectors using spare printheads or nozzles. In one embodiment, the control software may also exclude sectors with missing identifier errors from downstream processing steps so that such incomplete sectors are not included in the final identifier library. [0197] The identifier library to be assembled is specified and transmitted to the PFS via a set of specification files. The identifier library to be generated may be specified in a set of smaller units called blocks. The specification files comprise a write specification file containing the scheme to be used to assemble the identifier library from DNA components, a list of scheme-specific parameters, and a list of block specification file names. A block specification may comprise a block metadata file and a block data file. A block metadata file describes information about a block such as its length, hash, and other constructer-defined parameters. A block data file specifies the set of identifiers to be generated by the PFS . The block data file may be compressed using a data compression algorithm. The identifiers comprising a block may be specified in the form of a serialized data structure such as, but not limited to, a tree, a trie, a list, or a bitmap.

[0198] For example, an identifier library to be generated using the product scheme may be specified with a block metadata file containing the component library partition scheme, and a list of names of the possible components to be used in each layer. The block data file may contain the identifiers to be generated organized as a serialized trie data structure in which each path from the root to the leaf of the trie represents an identifier and each node along the path specifies the component name to be used in that layer of that identifier. The block data file may comprise a serialization of this trie by traversing it in order starting with the root, and visiting the left child node of each node, before visiting the node itself, and then visiting its right child node.

[0199] The PFS may monitor an input queue for incoming specification files. Upon detecting a new specification, the PFS may read the write specification and program itself with the necessary component supplied to the appropriate printheads or nozzles. The PFS may read the block metadata and data files, and process them to generate print instructions for printheads. The PFS may send these instructions for each block to the printheads and obtain status information for each sector from the printheads. Sectors that failed to print correctly or completely may be reported into a log and may be automatically reprinted.

Exemplary PFS

[0200] Fig. 1 illustrates a system for storing digital information in DNA by assembling DNA identifiers from components in rapid and high throughput manner using inkjet printing, for example, thermal inkjet printing, bubble inkjet printing, and piezo-electric inkjet printing. The system and its different implementations, henceforth referred to as the "Printer-Finisher System" or PFS, can comprise two sub-systems, a printer 120 and a finisher 130. In some implementations, the two subsystems 120, 130 may be attached and dependent on each other for individual function. In other implementations, the two subsystems 120, 130 may be disjoint and capable of functioning independently.

[0201] The printer 120 comprises rows of printheads 122, each containing DNA components (or copts) in solution, or in some implementations, dried DNA components. We may refer to each aqueous solution of distinct DNA component as an "ink" or a "color". The printheads 122 may programmably (in an on-demand manner) dispense pL-scale droplets onto coordinates of a substrate (or web, or webbing). The coordinates may be at 1 micrometer (um) in diameter/ spacing, 10 um in diameter/spacing, 50 um in diameter/spacing, 100 um in diameter/spacing, 150 um in diameter/spacing, 200 um in diameter/spacing or more. Inputs to printer system 120 include aqueous components/substrate. Outputs from printer system 120 include dry multi-layer spots on substrate. The environment of printer 120 may be dry (evaporative).

[0202] The finisher 130 comprises an instrument part (e.g. printhead) for dispensing reaction mix (e.g. ligase mix) for assembling components into identifiers. Inputs to finisher system 130The finisher 130 may dispense reaction mix onto each coordinate of a substrate (or web, or webbing). The finisher 130 may then incubate the reactions, thus enabling assembly, prior to consolidating the assembled identifiers from the substrate into a single pool 132. In some implementations, the reaction mix may be dispensed as part of the printer, not the finisher. In other implementations, the reaction mix may be dispensed to each coordinate prior to the DNA components. In some embodiments, a visible dye may be incorporated into the reaction mixture.

[0203] A substrate (or web) 136 may be automatically passed through the printer and finisher with linear (one-dimensional) movement. Linear movement at a constant speed may be accomplished with a reel-to-reel system (roller to roller) 134. In some implementations, linear movement at a constant speed may be accomplished with a recirculating, or continuous, webbing. In some embodiments, linear movement at a constant speed may be accomplished using webbing following a snail path. See, e.g., FIG. 7. In some implementations, linear movement at a constant speed may be accomplished using webbing following a spiral path. In some implementations, linear movement at a constant speed may be accomplished using webbing following a 180° twist path. For instance, the webbing will undergo a 180° turn at each roller with the system, wherein the webbing will pass all rollers right-side up. In other implementations, the substrate may be fixed and the printheads may move over the substrate in two dimensions (for example in a raster pattern).

[0204] FIG. 2 shows the printer subsystem 120 in more detail. The printer base 121 includes a printer base with a web drive hosting print engine 122, spot imager 126, and spot dryer 128. The print engine prints and over-prints to support the addressing scheme. The print engine 122 may comprise printheads. The printheads are designed to overprint or collocate or overlay different components to the same coordinates on the web 136. A single nozzle, a single printhead, a plurality of nozzles, a plurality of printheads or any combination thereof may overprint components onto the same coordinates. In addition to printheads, the printer may optionally comprise a register 124, a spot imager 126, and a spot dryer 128.

[0205] Registration includes spot alignment (if a multi-pass system). The register 124 is intended to maintain alignment between coordinates of the substrate and the printheads. This may be achieved by labeling the substrate with special markings that enable the register to track the motion of the substrate in real-time. In other implementations, the registration may be achieved by dead-reckoning the substrate position from encoders on the rollers. Control of alignment along the web may be done by timing the dispense actions from the print heads. Alignment across the web may require either the substrate or the print heads to move using an actuator.

[0206] The spot imager 126 provides verification of component addition. The spot imager 126 may be a camera intended to verify the proper dispense of components or reaction mixtures. To facilitate the function of the spot imager 126, a visible dye may be incorporated into the component inks or reaction mixture.

[0207] The spot dryer 128 is intended to desiccate the printed droplets so that they may be dried either in between printheads or upon exiting the printer (for example if the substrate is intended to be rolled upon exiting the printer). Desiccating droplets in between printheads may be useful for preventing liquid from overflowing in a particular coordinate during the over-printing process. Each printhead may dispense a droplet of at least 1 pL, 5 pL, 10 pL, 20 pL, 30 pL, 40 pL, 50 pL, or more. In some implementations, at least 1, 5, 10, 20, 50, 100, or more printheads may dispense into the same coordinate.

[0208] The printer subsystem may optionally include a substrate and coating module 129. The substrate and coating module 129 includes web material plus coating/patterning. The substrate may comprise a material or be coated with a material such as a low binding plastic like polyethylene terephthalate (PET) or polypropylene. [0209] FIG. 3A-3D depicts an example of a printhead 300 in a printer (e.g., printer 120 of FIG. 1). A printhead may contain 1, 2, 3, 4, or more inks (distinct component solutions). In this particular example, we consider a printhead 300 that may contain up to 4 inks with one ink provided for each row of nozzles. Additionally printheads may contain multiple nozzles per ink, for example 300 nozzles. In certain instances, the set of web coordinates addressable by some or all nozzles may be disjoint because the nozzles may not be suitably aligned so that each ink may over-print onto the same coordinate of a substrate passing linearly through the printhead. Or, the nozzles for different inks may not be appropriately spaced to print with a desired pitch. To resolve these issues, the printhead may be mounted at an angle (relative to the motion of the web) to enable overprinting of component inks at a desired pitch. As illustrated in FIG. 3B-D, a ~9 degree rotation is sufficient to enable overprinting of 4 inks with 167 um pitch. Specifically, FIG. 3C shows four rows of printerhead nozzles 302, 304, 306, 308. Each of rows 302, 304, 306, 208 may dispense a different component. Substrate 312 (which extends diagonally upward and to the right from the line pointed at by arrow 312) is moved linearly under printhead 300. Because of the 8.7 degree rotation of the printhead, a coordinate 314 on substrate 312 will pass directly beneath nozzles in rows 302, 304, 306, 308 along line 307 such that each nozzle may deposit a component on coordinate 314. As shown in FIG. 3D, multiple printheads 300, 310, 320 may be arranged in parallel to allow for printing on multiple substrates simultaneously. In an example, the printheads may be actuated to bring them into an alignment suitable for overprinting. The printheads may be MEMS (micro-electro-mechanical systems) thin film piezo ink jet heads or MEMS thermal inkjet head. Additives may be added to the component inks to facilitate compatibility with the printheads. For example, solutes like tris may be added to increase conductivity. As an example, humectants or surfactants (e.g. glycerol) may be added to improve ejection quality and printhead nozzle lifetime.

[0210] FIG. 4 depicts potential arrangements of the printheads within the printer. It is assumed that the substrate is passing in the longitudinal direction so that printheads on different tracks (T1 through T4) are printing onto independent coordinates, but that printheads along the same track may be printing onto the same coordinates (over-printing) on the substrate. The substrate may be passed through the printer multiple times, each time with new printheads (or the same printheads filled with new inks) in order to receive more DNA components per coordinate. However, if a large enough number of printheads are placed along each track then a single pass may be all that is necessary to incorporate a sufficient number of components for the desired number of identifiers to be built. For example, if identifiers are constructed from the product scheme of 10 layers of 8 components each (enabling 8 ¹⁰ identifiers, enough to store over a gigabit of data), and each printhead can print 4 components, then mounting 20 printheads along a track can be sufficient to enable all component set collocations in a single pass over the substrate. Multiple tracks may enable more efficient use of the substrate (web), allowing it to be shorter and allowing the identifiers to be built in a more high-throughput manner. If there is more width (latitudinal) in the substrate than there are tracks, then the substrate (or printhead chassis) may be shifted latitudinally after each pass to enable printing onto empty substrate along the width of the substrate instead of along the length. In another embodiment, separate printer base systems may print onto disjoint portions of the same substrate.

[0211] FIG. 5 demonstrates an example set up for the spot imager in the printer subsystem. The spot imager may use a line scan inspection principle. For example, the spot imager may include a computer system 520, a display 510, a line scan camera 530, a rotating drum 540, and an encoder 550. Computer system 520 is in communication with line scan camera 530. For example, computer system 520 may send control signals to line scan camera 520 and line scan camera 530 may send image data back to computer system 520. Computer system 520 and line camera system 530 may be communicate via a wireless or wired connection. The image data collected via line scan camera 530 is displayed at display 510. As shown in FIG. 5, line scan camera 530 may capture an image of drum 540 which may then be displayed on display 510. [0212] FIG. 6 shows the finisher subsystem 130 in more detail. Finisher substystem 130 comprises a finisher base 140 with a web drive, incubation buffer and hosting of dispense, spot humidifier 144, spot imager 146, and pooling subsystem 148. In addition to a part that dispenses reaction mix onto each coordinate of a substrate, the finisher may also comprise a part 142 that dispenses a reaction inhibitor onto each coordinate of a substrate 136 prior to consolidation. These dispensing parts may be printheads. They may be on-demand printheads, but continuous printing may also be sufficient as each coordinate along the web may be expected to receive a dispense. The dispense volume should be sufficient to cover the area of each coordinate where DNA components were previously dispensed. The dispense volume may be at least 1 pL, 5 pL, 10 pL, 20 pL, 30 pL, 40 pL, 50 pL, 60 pL, 70 pL, 80 pL, 90 pL, 100 pL, 150 pL, 200 pL, or more. The printheads may be MEMS (micro-electro-mechanical systems) thin film piezo inkjet heads or MEMS thermal inkjet head. Additives may be added to the dispensed liquids (e.g. master mix or inhibition mix) to facilitate compatibility with the printheads. For example, solutes like tris may be added to increase conductivity. As another example, humectants or surfactants may be added to improve ejection quality and printhead nozzle lifetime. Further, humectants like glycerol or polyethylene glycol (PEG) may be added to control evaporation both at the nozzle-air interface, as well as after the droplet has been dispensed. These humectants may further benefit the reaction mix by increasing reaction product yield.

[0213] Similar to the printer subsystem, the finisher may also comprise a register and a spot imager 146 to align the web with printheads and to validate proper dispensing, respectively. To facilitate the function of the spot imager, a visible dye may be incorporated into the dispensed fluids.

[0214] The finisher may further comprise several loops of rollers (configuration of rollers intended to loops the webbing) 134 after the reaction mix dispense so that the reaction on the web (substrate) 136 may incubate for a longer period of time prior to reaction consolidation. The finisher may comprise a fixed internal temperature that is optimal for reaction incubation; for example 4, 12, 25, 37, or more degrees Celsius. To slow control the evaporation of the dispensed reaction mix during the incubation phase, the finisher may comprise a fixed, high humidity level. The humidity level of the finisher subsystem 130 may be controller by spot humidifier 144 that controls maintenance of wet spots through the incubation period (e.g., while the substrate passes over rollers 134).

[0215] Lastly, the finisher may comprise a pooling system 148 to consolidate all of the identifier assembly reactions into one container after the incubation. Reaction inhibition may occur prior to this step, or it may occur during this step.

[0216] FIG. 7 shows an example of a loop of rollers 710, 720 for passing the web through the finisher during the incubation phase. The looping of the web enables longer incubation within a more confined space. For example, if the web is moving through the system at 180 mm/s, then ~60m of incubated web length is necessary of a 5 minute incubation time, but several loops may enable this length to incubate in a more confined space rather than a linear tunnel of ~60 m. Shorter incubation times may permit shorter incubated web lengths. For example, 45 second incubation times may permit ~9m of incubated web length and 10 second incubation times may permit ~2m of incubated web length. At these shorter incubated web lengths, less web loops may be necessary to confine the incubation within a small space.

[0217] Because of the geometry of the roller loops, the webbing 740 may pass certain rollers 720 right-side up and other rollers 710 upside down.

[0218] The bottom of the figure demonstrates the cross section of a roller 710 along the movement path of the web. The roller may be designed to contain valleys (or grooves, pockets, or any other indentation)730 between contact points of the substrate 740 so that the reactions (e.g., a coordinates where components were dispensed) may pass through the valley uninterfered. Alternatively the web may be rotated 180 degrees between rollers so that it always passes over the rollers in a right-side up configuration (i.e. 180° twist path). Alternatively the webbing may travel a spiral path through the incubator such that the circular path of the webbing around a set of rollers ensures that the side of the webbing containing reactions does not make contact with the rollers. As an analogy, consider winding a ribbon around a cylinder or applying grip tape to a tennis racquet.

[0219] In some implementations, the webbing is recirculating, or continuous, webbing. In some implementations, the webbing is a reel-to-reel system (roller to roller). In some implementations, the webbing follows a snail path. See, e.g., FIG. 7. In some implementations, the webbing follows a spiral path. In some implementations, the webbing follows a 180° twist path. For instance, the webbing will undergo a 180° turn at each roller with the system, wherein the webbing will pass all rollers right-side up configuration.

[0220] FIG. 8 illustrates the effect of reaction mix glycerol composition and finisher humidity on the anticipated equilibrium volume during incubation. The particles represent water molecules transitioning between liquid and gaseous phases. The droplet 820 represents a dispensed reaction on the web 810. The outer-shaded region represents water, the middle-shaded region represents glycerol and the inner-shaded region represents solute (e.g. DNA, enzyme/ligase, salt/magnesium, Tris). High humidity and high glycerol conditions will result in an equilibrium reaction composition that is most similar to the original composition. However, changes in reaction composition at equilibrium may be beneficial. For example, an increased relative amount of DNA components may lead to higher production yield of identifiers. Likewise, an increased amount of glycerol content may create a crowding effect that promotes identifier production. Though the reaction efficiency may be negatively affected by increases in certain solute (like salt) concentrations, the initial solute present in the reaction mix may be purposefully under-concentrated and designed to exist at optimal concentration after the reaction droplet evaporates to its equilibrium composition and volume.

[0221] FIG. 9 illustrates a pooling system that consolidates all reactions from the web into one container. A series of rollers 902 navigates the web 910 through a spray wash 914 and a collection reservoir 942 designed to capture reactions and their identifier products from the web 910. To prevent over-accumulation of volume in this process, the collection fluid may be continuously or iteratively flowed through a membrane designed to capture nucleic acids. For example, the membrane may be a silica membrane and the collection fluid may be DNA binding buffer 912 to facilitate the binding of nucleic acids to the membrane. The collection fluid may further comprise additives to inhibit the reactions so that they do not proceed in the consolidated volume. For example, if the reaction is a ligation reaction, then the collection fluid may contain EDTA (e.g. 25 mM) to chelate Magnesium ion from the ligase and therefore inhibit the reaction. The binding buffer could in one embodiment be recirculated through one or more binding columns to minimize the volume of binding buffer. The web 910 may be wetted with liquid to remove DNA from the web 910 and this may be combined with submerging the web 910 in liquid within the collection reservoir. Agitation of the web 910 or liquid (for example mechanical, fluidic or ultrasonic) and/or heating may be used to promote release of the DNA from the web 910. The scraper 918 could be a physical scraper, a liquid jet or a gas (e.g. air) jet, again to aid removal of DNA from the web 910. One or more sprays could be used to aid release of DNA from the web 910.

[0222] After the DNA is captured on the membrane, it may be removed from the system (machine) for elution and further evaluation. Further evaluation may comprise running the DNA on a gel and selecting for the band size corresponding to the expected identifier length (thereby purifying identifiers from other potential off-target products). In this example, the target identifier length is 300 bp. The DNA output may optionally be passed through a gel or other filtration 940 resulting in DNA data 930 that may be freeze dried.

[0223] Instead of reaction mix being added and inhibited prior to or during pooling, there is another embodiment of this system in which the reaction occurs in the pooling step. In this embodiment, components are annealed but not assembled during the incubation process, and then they are consolidated together in the pool which contains the reaction mix and proper environment conditions (e.g. temperature, pH, salts) for component assembly into identifiers. This embodiment may enable shorter incubation time on the web 910 and less stringent hardware requirements in the finisher, as once the annealed components are pooled, the rest of the reaction may proceed outside of the system (machine). In this embodiment, in order to prevent unwanted cross-assembly between components of different identifiers in the pooled reaction, special care may be taken to ensure that components are strongly annealed to each other prior to and during the pooling. This may involve using components with long sticky ends (and hybridization regions) for strong annealing as well as using lower temperatures in the pooling step to maintain annealed products and to restrict diffusion of un-annealed products.

[0224] FIG. 10 depicts a schematic of an embodiment of the data transfer pipeline through the PFS. FIG. 10 starts at source stream 1002 which contains 1 Tb of data. Source stream 1002 is transferred to codec 1004 and fed into job module 1006. Job module 1006 creates a job file, a block record, and block data for each source stream and/or codec file. This information is fed to block monitor 1008. Job module 1006 is monitored by job monitor 1016 which communicates with block monitor 1008. Block monitor 1008 watched for new blocks, verifies blocks and adds them to the pipeline for printing. The block data 1010 from job module 1006 is separated out and sent to block reader 1012 which processes the necessary ink and printhead configuration to print the block data. The block data is then transformed to printable frames 1014 that include the block data 1010 and “chirps” configured to test the accuracy of the data transfer. The frames 1014 are then sent to document printer module 1018 that communicates with printer 1034. For example, document printer module 1018 sends frames 1014 to printer 1034 to print and printer 1034 sends feedback to document printer 1018. Any failures 1020 are communicated to finish controller 1022 which are written to a text file or other storage method 1024. In additional to electronically communicating with document printer 1018, the printer 1034 receives the physical web sectors 1036. The web sectors 1036 are positionally verified by markers at one corner.

Each webs sector has a unique ID code. Printer 1032 deposits components 1032 onto the web.

The web then continues to the finisher 1026. Finisher 1026 communicates with finish controller 1022. Finish controller 1022 sends information regarding frames or partial frames to finish to finisher 1026 and finisher 1026 sends feedback back to finish controller 1022. Feedback from both the printer and finisher systems 1034, 1026 facilitates recording of the frame to sector allocating, coordination of web registration with printing and quality control, and recording of unsuccessful frames. After leaving the finisher 1026, the web has been printed and finished 1028 resulting in a substrate with DNA spots 1030 that may then be sent to a polling system or any other suitable storage method.

[0225] FIG. 11 illustrates an embodiment of the PFS that comprises four modules: a chassis module, a print engine module, an incubator module, and a pooling module. The function of the chassis module may be to provide a base system that drives, stabilizes, and controls the movement of webbing through all modules of the system. The function of the print engine module may be to print DNA components as well as other materials and reagents into reaction droplets on the webbing. The function of the incubator module may be to provide time and environmental control for improved product (e.g., assembled DNA or identifier) yield in the reaction droplets. The function of the pooler module may be to remove reaction droplets from the webbing and consolidate them into one container.

[0226] In some embodiments, the reaction droplets may assemble DNA identifiers through enzymatic ligation. In some embodiments, the reaction droplets may assemble DNA identifiers through click chemistry.

[0227] In some embodiments, the incubator module may comprise 100, 50, 25, 10, 5, 1, or .1 meters of webbing or less. In some embodiments, the PFS may not have an incubator module. [0228] In some embodiments, the print engine or incubator may contain intermittent printheads or dispensing submodules to replenish volume in the reaction droplets as they evaporate on the webbing. [0229] In some embodiments, the webbing passing through the PFS may unwind from a roll prior to the print engine and re-wind on a roll after the pooler. In some embodiments, the webbing may form a continuous loop that passes back to the print engine after the pooler.

[0230] FIG. 12 illustrates an embodiment of the PFS that pools reaction droplets into an emulsion 1260. The emulsion 1260 may comprise oil or any liquid that is not miscible with the reaction droplets, thereby enabling the reaction droplets 1250 to maintain their contents, even after being pooled. The webbing 1220 of PFS may be coated with oil prior to passing underneath the printheads 1210 (e.g. via rollers 1230 and 1240). The reaction droplets 1250 may contain surfactants and other additives to control their size and shape in the emulsion. The surfactants and additives may also promote stability within the emulsion and prevent coalescence between different reaction droplets. The pooled emulsified reaction droplets may be passed through a microfluidic device. The pooled emulsified reaction droplets may be incubated. Moreover, the pooled emulsified reaction droplets may be aggregated and isolated from the emulsion.

[0231] FIG. 13 illustrates an embodiment of the PFS where reaction droplets 1350 are coated with oil (or another non-miscible liquid) 1370 after being printed onto the webbing 1320. The oil coating may occur with an oil dispense submodule 1380 that prints, dispenses, or sprays the oil on the reaction droplets 1350 as the webbing 1320 passes under printhead cluster 1310 via rollers 1330 and 1340. The oil may lessen or prevent evaporation of the reaction droplets on the webbing 1320. The reaction droplets may contain surfactants and other additives. The oil- covered reaction droplets 1370 may be pooled into an emulsion 1390. The pooled emulsified reaction droplets may be passed through a microfluidic device. The pooled emulsified reaction droplets may be incubated. Moreover, the pooled emulsified reaction droplets may be aggregated and isolated from the emulsion.

[0232] FIG. 14 illustrates an embodiment of the PFS where reaction droplets 1450 contain beads that bind the printed DNA components. The beads may be coated with silica, carboxyl groups, or amine or imidazole moieties that bind DNA. Alternatively or in addition, the beads may be coated with streptavidin that binds DNA components through a biotin linkage. The biotin may be linked to DNA components with a photo- or UV-cleavable linker.

[0233] The webbing 1420 may be ubiquitously covered with beads or patterned with beads prior to passing underneath the printheads 1410 (e.g., via rollers 1430 and 1440). Alternatively, or in addition, the beads may be deposited or printed into each of the reaction droplets 1450. The reaction droplets may contain additives that promote DNA binding to the beads. The beads may be at a quantity of 1, 2, 3, 5, 10, 20, 50, 100 or more per reaction droplet.

[0234] The reaction droplets 1450 may be pooled in a solution 1460 that prevents further association of DNA to the beads. The solution 1460may contain blocking agents such as BSA. The DNA-bound beads in the pooled solution may be separated from the solution and dried 1470. Separation may occur through centrifugation. In another embodiment, the beads may be magnetic and they may be separated with a magnet.

[0235] Pooled DNA-bound beads (dried 1470 or in solution 1460) may be further encapsulated in emulsified reaction droplets. In one embodiment, DNA-bound beads are each encapsulated in a reaction droplet using microfluidics. In another embodiment, DNA-bound beads are each encapsulated in a reaction droplet by mixing the reaction solution and oil (or another immiscible liquid) such that droplets spontaneously form. The ratio of spontaneously formed reaction droplets to DNA-bound beads may be tuned such that no reaction droplet is likely to contain more than one DNA-bound bead. The reaction droplets may contain surfactants or other additives to control their size or to prevent coalescence of other reaction droplets.

[0236] Reaction droplets may contain reagents that disassociate the DNA on the beads. The reaction droplets may contain reagents that ligate the DNA components together to form identifiers. The reaction droplets may contain enzymatic ligases as well as ligation co-factors such as ATP, DTT, or salts. [0237] If DNA is bound to the beads through a photo-cleavable or UV-cleavable linkage, the DNA may be released from the beads by exposing the emulsion to electromagnetic waves of the appropriate wavelength (e.g. light or UV).

[0238] FIG. 15 illustrates an example of how DNA components bound onto beads may be processed into identifiers using an emulsion. At step 1510 DNA-bound beads are provided. The DNA-bound beans are then emulsified at 1520 such that the DNA-bound beads encapsulated in reaction mix droplets are immersed in oil. The DNA is then dissociated resulting in mixture 1530. The dissociated DNA mixture is incubated, resulting in the assembled DNA of 1540.

[0239] While exemplary implementations have been shown and described herein, it will be obvious to those skilled in the art that such implementations are provided by way of example only. Numerous variations, changes, and substitutions will occur to those skilled in the art. It should be understood that various alternatives to the implementations described herein may be employed.

Example modifications to decrease the PFS size

[0240] As previously described in FIG. 11, the PFS may comprise four modules: chassis, print engine, incubator, and pooler. For the PFS that encodes 1 Tb of information in DNA, the approximate size of each module may be as listed in the table below:

Table 1. Approximate module size

Module L (mm) W (mm) H (mm)

Printer 1850 1200 2000

Incubator 2300 1150 2000

Chassis 800 1150 2000

Pooler 600 1150 1600 [0241] To decrease the size of the PFS, one may reduce the size of the individual modules or remove modules. Examples of modification to decrease size may include the following:

(1) Increasing print head capacity in the print engine. Either custom printheads or additional print heads may be used to allow for the number of nozzle columns to triple (or increase by a larger factor). This may triple the number of printed reactions as well as the print width on the webbing.

(2) Using recirculating webbing. For example, the PFS may use 21 kilometers of polypropylene webbing to print enough reactions to encode 1Tb of information. To eliminate the use of webbing reels (or rolls), recirculating webbing may be used as an alternative to roll-to-roll webbing. Recovery studies show that DNA can be readily removed from the web in the pooler.

(3) Decreasing ligation reaction time. This may facilitate the use of a smaller incubator or no incubator at all. To decrease ligation reaction time without sacrificing yield, the chemistry can be optimized to meet a higher ligation rate.

(4) Performing ligation at room temperature and ambient conditions. This may eliminate the need for an incubator module.

(5) Using oil emulsions to maintain reaction droplet volume or to enable ligation to start or continue after the pooler. This may eliminate the need for an incubator module.

[0242] While exemplary embodiments have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only.

Numerous variations, changes, and substitutions will occur to those skilled in the art. It should be understood that various alternatives to the embodiments described herein may be employed.

Applications of methods and systems of combinatorial DNA assembly

[0243] The methods and systems described herein for combinatorial assembly of components into large defined sets of identifiers have been described thus far as they relate to information technology (for example, data storage, computing, and cryptography). However, these systems and methods may more generally be used for any application of high throughput combinatorial DNA assembly.

[0244] In one embodiment, we may create a library of combinatorial DNA that encodes for amino acid chains. Those amino acid chains may represent either peptides or proteins. The DNA fragments for assembly may comprise codon sequences. The junctions along which fragments assemble may be functionally or structurally inert codons that will be common to all members of the combinatorial library. Alternatively, the junctions along which fragments assemble may be introns that are eventually removed from messenger RNA which is later translated into the processed peptide chain. Certain fragments may not be codons, but rather barcode sequences that (in combination with other assembled barcodes) uniquely tag each combinatorial string of codons. The assembled products (barcodes + string of codons) may be pooled together and encapsulated in droplets for in vitro expression assays, or pooled together and transformed into cells for in vivo expression assays. The assays may have a fluorescent output such that the droplets/cells may be sorted into bins by fluorescent strength and subsequently their DNA barcodes sequenced for the purpose of correlating each codon string with a particular output.

[0245] In another embodiment, we may create a library of combinatorial DNA that encodes for RNAs. For example, the assembled DNA may represent combinations of microRNAs or CRISPR gRNAs. Either pooled in vitro or in vivo RNA expression assays may be performed as described above with either droplets or cells, and with barcodes to keep track of which droplets or cells contain which RNA sequence. However, some pooled assays may be done outside droplets or cells if the output itself is RNA sequencing data. Examples of such pooled assays include RNA aptamer screening and testing (for example, SELEX).

[0246] In another embodiment, we may create a library of combinatorial DNA that encodes for genes in a metabolic pathway. Each DNA fragment may contain a gene expression construct. The junctions along which fragments are assembled may represent inert DNA sequences in between genes. Either pooled in vitro or in vivo gene pathway expression assays may be performed as described above with either droplets or cells, and with barcodes to keep track of which droplets or cells contain which gene pathways.

[0247] In another embodiment, we may create a library of combinatorial DNA with different combinations of gene regulatory elements. Examples of gene regulatory elements include 5' untranslated regions (UTRs), ribosome binding sites (RBSs), introns, exons, promoters, terminators, and transcription factor (TF) binding sites. Either pooled in vitro or in vivo gene expression assays may be performed as described above with either droplets or cells, and with barcodes to keep track of which droplets or cells contain which genetic regulatory constructs. [0248] In another embodiment, a library of combinatorial DNA aptamers may be created. Assays can be performed to test the ability of the DNA aptamers to bind ligands.

Example implementations of the printer-finisher technologies

[0249] Provided herein are systems and assemblies for storing digital information by assembling an identifier nucleic acid molecule from at least a first component nucleic acid molecule and a second component nucleic acid molecule. The system may include (a) a first printhead configured to dispense a first droplet of a first solution comprising the first component nucleic acid molecule onto a coordinate on a substrate; (b) a second printhead configured to dispense a second droplet of a second solution comprising the second component nucleic acid molecule onto the coordinate on the substrate, such that the first and second component nucleic acid molecules are collocated on the substrate; and (c) a finisher that dispenses a reaction mix onto the coordinate on the substrate to physically link the first and second component nucleic acid molecules, provides a condition necessary to physically link the first and second component nucleic acid molecules, or both. Generally, the first and second printheads may be part of a system including rows of any number of printheads and corresponding nozzles that print or dispense various components.

[0250] In some implementations, the identifier nucleic acid molecule is represents a position and a value of a symbol in a string of symbols. For example, each symbol in the string may have a corresponding identifier that represents the corresponding symbol position. In particular, the identifier may be created if the corresponding value of the symbol is 1, while identifiers representing symbols having value 0 may not be created. When all identifiers for symbols in the string are created, the identifier molecules for the string may be combined within a pool, such that the presence of specific identifiers within the pool represents a 1 -value for corresponding symbol positions, while the absence of specific identifiers within the pool represents a 0-value for corresponding symbol positions. The alternative approach may be taken, in which identifiers may be created for corresponding symbol values of 0, while identifiers representing symbols having value 1 may not be created. In some implementations, the finisher includes a third printhead configured to dispense the reaction mix onto the coordinate on the substrate. The finisher may further comprise an incubator, a pooling system, or both. The incubator may provide a specific temperature condition or set of conditions that are needed for a reaction to proceed for assembling the components to form identifier nucleic acid molecules.

[0251] In some implementations, the finisher dispenses the reaction mix onto the coordinate before the first printhead dispenses the first droplet onto the coordinate, before the second printhead dispenses the second droplet onto the coordinate, or both. In general, the finisher may dispense the reaction mix onto the coordinate at any time, before any droplets are dispensed, after the first droplet is dispensed but before the last droplet is dispensed, or after all droplets are dispensed.

[0252] In some implementations, the system comprises at least one roller that moves the substrate past the first printhead, the second printhead, and the finisher. In some implementations, the roller provides linear movement of the substrate. In general, the roller may provide two-dimensional or three-dimensional movement of the substrate, which may pass each of the first and second printheads and the finisher only once, or multiple times. In some implementations, the roller is part of a reel-to-reel system that accomplishes the linear movement of the substrate at a constant speed. [0253] In some implementations, the substrate forms a continuous loop of material, and the at least one roller is part of a set of rollers that causes the coordinate on the substrate to pass the first printhead, the second printhead, and the finisher multiple times. In general, it may be desirable to configure the system such that the at least one roller does not contact any of the coordinates on the substrate, to prevent any rubbing or possible contamination of the materials being dispensed on the substrate. Particularly, the substrate has a first surface upon which the first droplet, second droplet, and reaction mix are dispensed, and a second surface opposite the first surface, and the at least one roller contacts the second surface and does not contact the first surface. Alternatively, even if at least one of the rollers contacts the first surface, the roller may be grooved in a manner to avoid contacting any of the coordinates where material is dispensed.

[0254] In some implementations, the system comprises a second roller comprising at least one valley, wherein the second roller contacts the first surface such that the at least one valley aligns with the coordinate. In some implementations, the system comprises a second roller, wherein the substrate is rotated 180 degrees between the at least one roller and the second roller or in a spiral path, such that the second roller contacts the second surface and does not contact the first surface. [0255] In some implementations, the coordinate has a diameter or spacing from other coordinates on the substrate of between 1 micrometer and 200 micrometers. In some implementations, the first and second droplets each have a volume between 1 pL and 50 pL.

[0256] In some implementations, the system comprises a register that tracks motion of the substrate in real-time to maintain alignment between coordinates of the substrate and the first and second printheads. In some implementations, the first and second solutions incorporate a dye, the system comprising a spot imager including a camera that verifies a proper dispense of the first and/or second droplets.

[0257] In some implementations, the system comprises a spot dryer that desiccates the first and second droplets on the substrate. In some implementations, the first printhead includes a first plurality of nozzles that dispense droplets of the first solution at different coordinates of the substrate. In some implementations, the first printhead includes a second plurality of nozzles that dispense droplets of a third solution at different coordinates of the substrate.

[0258] In some implementations, the system comprises a substrate. In some implementations, the substrate comprises a low binding plastic. In some implementations, the substrate comprises polyethylene terephthalate (PET) or polypropylene.

[0259] In some implementations, the first and second printheads are mounted within the system at an angle relative to motion of the substrate, wherein the angle enables overprinting on the coordinate. In some implementations, the first printhead is a MEMS thin film piezo inkjet head or a MEMS thermal inkjet head. In some implementations, the first and second printheads are positioned along a same track to dispense droplets onto the coordinate, the system comprising additional printheads that are positioned along at least one additional track to dispense droplets onto another coordinate in the corresponding track.

[0260] In some implementations, the finisher has a fixed internal temperature optimal for reaction incubation. In some implementations, the finisher has a fixed humidity level that controls the evaporation of the reaction mix during incubation. In some implementations, the finisher comprises a heater that heats the substrate before incubation to prevent condensation. In some implementations, the finisher includes a pooling system that consolidates multiple reactions from different coordinates on the substrate into a container. In some implementations, the finisher dispenses a reaction inhibitor onto the coordinate of the substrate before consolidation. [0261] In some implementations, the container contains a pooling solution a reaction inhibitor. In some implementations, the reaction inhibitor is ethylenediaminetetraacetic acid (EDTA).

[0262] In some implementations, the system comprises a membrane that captures nucleic acids from fluid collected from the different coordinates on the substrate. In some implementations, the system comprises a scraper that removes nucleic acid from the substrate. In some implementations, the multiple reactions from different coordinates are pooled together into an emulsion that enables the multiple reactions to maintain their contents after being pooled. [0263] In some implementations, the substrate is coated with a non-miscible liquid or oil. In some implementations, the system comprises an oil dispenser that dispenses oil on the coordinates. In some implementations, the substrate is coated or patterned with beads that bind the first and second component nucleic acid molecules. In some implementations, the system comprises a bead dispenser that dispenses beads on the coordinates.

[0264] In some implementations, the reaction mix comprises a ligase. In some implementations, the first solution, the second solution, and the reaction mix comprises an additive. In some implementations, the additive is configured to enable compatibility of the first solution with the first printhead, the second solution with the second printhead, or the reaction mix with the finisher. In some implementations, the additive mitigates evaporation of the of the first solution, the second solution, or the reaction mix. In some implementations, the additive comprises at least one of a humectant, a surfactant, and a biocide.

[0265] In some implementations, the system comprises a computer processor configured to execute instructions to operate the system. The instructions may include (1) a set of instructions for moving the substrate past the printheads, such as by controlling a set of rollers, for example, and (2) another set of instructions for specifying the times for each printhead or corresponding nozzle to dispense a solution.

[0266] In an aspect, the present disclosure provides a system for assembling a nucleic acid molecule, the system comprising: (a) a first printhead configured to dispense a first droplet of a first solution comprising a first component nucleic acid molecule onto a coordinate on a substrate; (b) a second printhead configured to dispense a second droplet of a second solution comprising a second component nucleic acid molecule onto the coordinate on the substrate, such that the first and second component nucleic acid molecules are collocated on the substrate; and (c) a finisher that dispenses a reaction mix onto the coordinate on the substrate to physically link the first and second component nucleic acid molecules, provides a condition necessary to physically link the first and second component nucleic acid molecules, or both. [0267] In some implementations, the finisher comprises a third printhead configured to dispense the reaction mix onto the coordinate on the substrate. The finisher may further comprise an incubator, a pooling system, or both. In general, the finisher may dispense the reaction mix at any time. Specifically, the reaction mix may be dispensed onto the coordinate before the first printhead dispenses the first droplet onto the coordinate, before the second printhead dispenses the second droplet onto the coordinate, or both.

[0268] In some implementations, the assembled nucleic acid molecules comprise gene-, peptide-, or RNA-encoding DNA. The assembled nucleic acid molecules may comprise a DNA aptamer library.

Noise Reduction

[0269] While various implementations of the noise reduction technologies have been shown and described herein, such implementations are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the implementations of the technologies described in this specification (“herein”) can be employed.

[0270] Described in this specification are technologies including systems, devices, and methods to write, store, read, and perform computation of digital information using nucleic acid molecules (e.g., DNA or RNA) in a low-to-no noise manner. The technologies include, for example, devices and methods to write and/or read digital information in nucleic acid sequences, e.g., using Next-Generation Sequencing (NGS) methods or methods using a nano-channel and a sensor to detect one or more components of the translocating nucleic acid strand.

[0271] Methods and systems of the present disclosure can be used to encode computer data or information in a plurality of “identifiers,” each of which can represent one or more bits of the original information, e.g., as described above. These identifiers can include two or more building blocks called “components,” each component having a nucleic acid sequence. A prefabricated set of components may be divided into “layers.” For example, each individual identifier may be constructed by concatenating one component each from a plurality of layer in a fixed order. The order can be predetermined or random. The identifiers can be assembled, using chemical techniques, e.g., ligation techniques, as described above in this specification. The identifiers are produced with techniques disclosed herein so as to minimize or eliminate presence of unligated or incompletely ligated oligonucleotides, called “fragments” in the final product. These unintended, truncated identifiers/oligonucleotides that are the result of the ligation process are later amplified (e.g., using PCR) and cause noise in the system. The presence of unligated and incompletely ligated products (unligated components and/or fragments) can result in spurious products that are generated during PCR via recombination (a process during which two oligonucleotides are joined at an overlapping region and create a new, unintended chimeric product during PCR). The presence of unligated or incompletely ligated products can generate unintended truncated identifiers by acting as primers, contributing to noise. These products can act as competing templates for PCR and can result in a reduced signal for full-length identifiers (FLIs). Moreover, the presence of these unligated products can interfere with qPCR quantification.

[0272] Existing technologies involve extra-solution processes for removal of these products, e.g., DNA purification methods (silica and/or anion exchange columns, Solid Phase Reversible Immobilization (SPRI) beads, and/or gel extraction) and/or nuclease treatment. These existing technologies, which focus on removal of unligated and incompletely ligated products, are inefficient, leaving behind enough unligated and incompletely ligated products to still affect PCR while also potentially resulting in loss of full-length identifiers. Difficulties with purification and sequence precision can be even more pronounced in systems that attempt to process ten or more nucleotides.

[0273] The technologies described in this specification address this problem. The technologies include methods including blocking PCR extension as a mechanism for improving decodability and reducing noise. The technologies include methods including blocking PCR extension to improve qPCR quantification. The technologies include methods of use of ddNTPs to prevent recombination. The technologies provide flexibility in use and can be used in conjunction with any existing purification method, without affecting signal. Post-ddNTP treated PCR is compatible with most polymerases.

[0274] In an aspect, the present specification provides technologies for writing information (e.g., digital information) into nucleic acid molecules so as to reduce or minimize potential noise arising from incomplete ligation by modifying the nucleic acids with ddNTPs, polymerases, and/or other enzymes that block the creation or amplification of chimeric fragments. Example methods include steps of (a) generating a string of symbols to represent digital or other information; (b) constructing a plurality of components as described in this specification, where each individual component of the plurality of components comprises a nucleic acid sequence; (c) chemically linking together two or more components of the plurality of components, e.g., via at least one sticky end of the individual component of the two or more components, thereby generating a plurality of identifiers, where each identifier of the plurality of identifiers includes two or more components. An individual identifier of the plurality of identifiers corresponds to an individual symbol in the string of symbols. The method includes selectively capturing or amplifying an identifier library including at least a subset of the plurality of identifiers.

[0275] The information, e.g., digital information, stored in nucleic acids (e.g., identifiers) is accessed through sequencing or hybridization assays. For example, primers or probes can be designed to bind to common regions or barcoded regions of the nucleic acid sequence. This technique can provide amplification of any region of the nucleic acid molecule. The amplification product can then be read by sequencing the amplification product or by a hybridization assay.

[0276] PCR based methods can be used to access and copy data from identifier or nucleic acid sample pools. A primer is a relatively short single-stranded nucleic acid that can be used to initiate DNA synthesis. Using common primer binding sites that flank the identifiers in the pools or hyper-pools, nucleic acids containing information can be readily copied. Alternatively, other nucleic acid amplification approaches, such as isothermal amplification, can also be used to readily copy data from sample pools or hyper-pools (e.g., identifier libraries).

[0277] Current methods to remove incompletely assembled fragments (e.g., gel extraction) can result in a significant loss of full-length product, but still carry over a large quantity of unligated products that can act as primers during PCR, thereby generating noise. Therefore, preventing PCR extension from these small fragments can be an important mechanism for reducing noise and improving decodability of the identifiers.

[0278] This specification includes technologies to modify nucleic acid molecules to (1) prevent or reduce undesired PCR amplification of unligated products (components or fragments) and (2) noise reduction by removing undesired products from a reaction volume prior to PCR amplification.

Preventing or reducing undesired PCR amplification

[0279] This specification includes technologies to modify nucleic acid molecules (e.g., components or fragments) to incorporate dideoxynucleotides (ddNTPs) on the 3 ’-ends of all nucleic acid molecules. The 3’ end of a nucleic acid molecule is a region where a PCR primer attaches to a target molecule. ddNTPs are inhibitors of DNA polymerase and are used in Sanger sequencing. Sanger sequencing is a method of DNA sequencing is based on the random incorporation of fluorescently labeled ddNTPs by DNA. These ddNTPs are labeled for each of the four deoxynucleotides (ddATP, ddCTP, ddGTP, ddTTP) and are thus used to identify the terminal nucleotide in a DNA sequence. Sequential PCR followed by gel electrophoresis yield labeled DNA fragments of varying lengths that provide sequence information of the sample DNA. In contrast, the technologies described in this specification do not use fluorescently labeled ddNTPs to determine a nucleotide sequence, but utilize ddNTPs to selectively control and inhibit PCR extension from modified fragment molecules, thereby minimizing the formation of spurious products that are generated via recombination (e.g., nucleic acid molecules composed of parts of two or more different sequences brought together during PCR). An edge component (a nucleic acid molecule that constitutes or includes an end of a fully assembled identifier (FLI)) is left unmodified by ddNTP at its terminal end to allow PCT amplification of the full-length identifier. [0280] FIG. 16 illustrates the principle of this technology. The reduction or elimination of spurious product can reduce noise after PCR and therefore improve decodability of the information encoded in the identifiers. Moreover, the cessation of PCR extension from these nucleic acids or fragments can reduce or prevent the amplification of partial products due to unligated products acting as primers. These partial products may act as competing templates during PCR (reducing primer availability for full length products) and may result in a reduced signal for full length identifiers. Therefore, blocking PCR extension from unligated or incompletely ligated products can also improve PCR efficiency, improving full length identifier yield.

[0281] FIG. 17 shows an attempt to amplify an example 360 base pair (bp) product using two sets of primers that contain the same sequence. In lane 3, these primers contain no modifications, however in lane 6 both primers contain a ddNTP on their 3’ end. No signal can be seen in lane 6, which demonstrates that the presence of a ddNTP on the 3’ end of a primer prevents amplification from that primer. The technologies described in this specification include methods for adding ddNTPs to the 3’ ends of molecules that unintentionally act as primers, e.g., incompletely assembled oligonucleotides that are not intended to be formed through the process. [0282] Described in this specification are three example ways of generating these ddNTP ends: (1) Terminal transferase-based incorporation of ddNTPs, (2) End-fill-in using DNA polymerases, and (3) Blunting and ddATP tailing;.

1. Terminal Transferase based incorporation of ddNTPs

[0283] In some implementations, the technologies described in this specification include the use of template-independent polymerases for incorporation of ddNTPs. Template-independent polymerases, such as members of the X-family of polymerase enzymes, do not require a template molecule to synthesize DNA (e.g., by synthesizing the reverse complement strand of a DNA strand). One suitable polymerase is terminal transferase (TdT), a template independent polymerase that adds nucleotides to the 3’ end of DNA molecules. TdT can act on protruding, recessed, and/or blunt ended molecules of DNA and lacks exonuclease activity. Therefore, the addition of ddNTPs via TdT (and/or another template-independent polymerase) can act as a mechanism of adding ddNTPs to the ends of molecules, thereby preventing their ability to act as primers. This technology therefore differs from other technologies using TdT, e.g., methods for controlled de novo synthesis of oligonucleotides for data encoding using TdT-mediated iterative DNA assembly from deoxynucleotide triphosphates (dNTPs).

[0284] To help detect successful incorporation of ddNTP, a combination of ddNTPs and dNTPs can be used. In an example process, a reaction volume includes a plurality of components of one or more layers. The components including a plurality of edge components. The components have 3’ overhangs. A volume containing template-independent polymerase (e.g., TdT) and a volume containing one or more ddNTPs (e.g., ddATP, ddCTP, ddGTP, or ddTTP) are added. In some implementations, a volume containing one or more dNTPs (e.g., dATP, dCTP, dGTP, or dTTP) are added. The TdT reacts with the components and attaches a ddNTP and/or dNTP, e.g., to the 3 ’-ends of the components. In some implementations, the ends of the edge components that are configured to be the terminal ends of the FLI are modified, e.g., to protect FLIs from the noise reduction processes described below (e.g., using hairpin loops at the terminal ends). To ligate the components, T4 Ligase, ATP, and/or other appropriate ligation reagents are added to the volume. The ligation reaction yields a volume containing a set of oligonucleotides including components, fragments, and FLIs. In some implementations, following the ligation reaction, the terminal ends are de-protected, e.g., hairpins at the terminal ends of the edge components are removed, e.g., using DNA-dependent protein kinase catalytic subunit (DNA- PKcs) and Artemis (a structure-specific endonuclease). Subsequently, PCR primers are hybridized to the oligonucleotides. The oligonucleotides are then subjected to PCR amplification. Any chimeric component or fragment with a terminal ddNTP is not amplified due to the inhibition of DNA polymerase by ddNTP, nor can modified components or fragments act as PCR primers. This process increases the signal (FLI) to noise (components, fragments) ratio of the DNA coding/decoding process. The chemical process can be performed, e.g., in a batch processing method or in a microfluidic device. After PCR amplification, the oligonucleotides can be sequenced, and the information encoded therein can be read.

[0285] Automated electrophoresis (e.g., Agilent® Tapestation®) results are shown in FIG. 18A-18C. FIG. 18A shows results for ligation of 9 layers (nucleic acid components). FIG. 18B shows results for 9-layer ligation of components treated with just dNTPs. FIG. 18C shows results for 9-layer ligation of components treated with ddNTPs and dNTPs. FIGS. 18A-18C show that ddNTPs can be successfully incorporated by TdT as ddNTPs prevent the extension of the long 3’ tails that are generated by TdT incorporation of dNTPs, as evidenced by the peak intensity of over 60, representing the large number of molecules over about 1500 bp (dashed box in FIG. 18B.). Without ddNTPs, the majority of molecules within the 50-500 bp range (dashed box in FIG. 18A) would “shift” to the 1500+ bp range (FIG. 18B). Successful incorporation of ddNTPS is demonstrated in FIG. 18C where ddNTPs prevents uncontrolled ligation resulting in large multilayer oligonucleotides (as evidenced by the lack of shift in peaks from the 50-500 range to the 1500+ bp range as shown in FIG. 18B).

[0286] The use of a combination of ddNTPs and dNTPs was also tested on a 16-layer, 129,572 identifier library generated by an example DNA writer as described above in this specification. Table 2 shows data demonstrating an increase of formation of desired product (1- sym observations), a reduction in the formation of undesired (e.g., chimeric) products (0-sym observations), and nearly 25% improvement in SNR following ddNTP treatment using TdT in a DNA writer-generated library. Table 2

2. End Fill-in incorporation of ddNTPs

[0287] In some implementations, the technologies described in this specification include End Fill-in incorporation of ddNTPs. An example end fill-in method includes the use of a DNA polymerase (e.g., T4 polymerase, Therminator DNA polymerase, TdT, Klenow fragment, T7 polymerase, Sulfolobus DNA Polymerase IV, DNA Polymerase I (E. coli)), a reaction buffer, and ddNTPs.

[0288] In some implementations, nucleic acid molecules (e.g., identifier components) are designed such that they result in having 3’ overhangs. In some implementations nucleic acid molecules (e.g., identifier components) are designed such that they include 5’ overhangs (FIG. 19). In some implementations of the technology that use polymerases, 5’ overhangs may be required because polymerases carry out DNA synthesis in a 5’ - 3’ manner. Because the sequence composition is not affected, any adjustment of component synthesis (e.g., conversion from a 3’ overhang to a 5’ overhang) has no impact on any applicable encoding/decoding methods.

[0289] In an example process, a reaction volume includes a plurality of components of one or more layers, the components including a plurality of edge components. The components have 5’ overhangs. A volume containing a polymerase (e.g., T4 polymerase, Therminator DNA polymerase, TdT) and a volume containing one or more ddNTPs (e.g., ddATP, ddCTP, ddGTP, or ddTTP) are added. In some implementations, a volume containing one or more dNTPs (e.g., dATP, dCTP, dGTP, or dTTP) are added. The ddNTPs/dNTPs are added to the 3’ ends of the components by hybridization to the 5’ overhangs. In some implementations, the ends of the edge components that are configured to be the terminal ends of the FLI are modified to protect FLIs from the noise reduction processes described below (e.g., e.g., using a hairpin loop at the terminal ends). Example reaction conditions for end fill-in reactions include incubations at 12° C for 15 mins. After incubation, the product is purified (e.g., using gel extraction, silica columns, alcohol precipitation, or magnetic SPRI beads) to ensure ddNTPs are not carried over into future reactions. To ligate the components, T4 Ligase, ATP, and/or other appropriate ligation reagents are added to the volume. The ligation reaction yields a volume containing a set of oligonucleotides including components, fragments, and FLIs. In some implementations, following the ligation reaction, the terminal ends are de-protected, e.g., the hairpins at the terminal ends of the edge components are removed, e.g., using DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Artemis (a structure-specific endonuclease). Subsequently, PCR primers are hybridized to the oligonucleotides. The oligonucleotides are then subjected to PCR amplification. Any chimeric component or fragment with a terminal ddNTP is not amplified due to the inhibition of DNA polymerase by ddNTP, nor can modified components or fragments act as PCR primers. This process increases the signal (FLI) to noise (components, fragments) ratio of the DNA coding/decoding process. The chemical process can be performed in a batch processing method or in a microfluidic device. After PCR amplification, the oligonucleotides can be sequenced and the information encoded therein can be read.

[0290] The end-fill in reaction can be integrated into a nucleic acid post-processing workflow, e.g., without the need for additional purification steps. FIG. 20A illustrates integration of the noise reduction step in an “excised run” workflow, e.g., a workflow including excision of a band of gel containing the nucleic acids of interest, e.g., as described above. FIG. 20B illustrates integration of the noise reduction step in an “pooler run” workflow, e.g., a workflow using a pooling system as described above in this specification. Moreover, as the end-fill in reaction is carried out prior to qPCR, end fill-in incorporation of ddNTPs can result in a more specific signal for quantification of full-length identifiers. In some implementations, e.g., depending on the efficiency of the post-processing methods used, ddNTP incorporation can be carried out after gel extraction.

3. Blunting and ddATP tailing

[0291] In some implementations, the technologies described in this specification include Blunting and ddATP tailing. This method of ddNTP incorporation includes two steps: the first step includes the removal of overhangs (blunting). This removal can be done using nucleases e.g., Mung Bean nuclease, Nuclease Pl, Exonuclease I, Exonuclease III, Micrococcal Nuclease, SI Nuclease, or polymerases that contain exonuclease activity. In some implementations, blunting can be carried out by filling in the overhangs, e.g., as described above. The second step includes the addition of a ddATP on the 3’ end of the now blunt molecules. This process can be carried out by polymerases, such as taq polymerase, Klenow fragment etc.

[0292] In an example process, a reaction volume includes a plurality of components of one or more layers. The components including a plurality of edge components. The components have 3’ overhangs or 5’ overhangs. In a first step, a volume containing nucleases (e.g., Mung Bean nuclease, Nuclease Pl, or polymerases that contain exonuclease activity) are added to remove the overhangs, e.g., by degrading or hydrolyzing the single-stranded extensions. In a second step, a volume containing a polymerase (e.g., taq polymerase, Klenow fragment) and a volume containing one or more ddATPs are added. In some implementations, the ends of the edge components that are configured to be the terminal ends of the FLI are configured to protect FLIs from the noise reduction processes described below (e.g., using a hairpin loop at the terminal ends). To ligate the components, T4 Ligase, ATP, and/or other appropriate ligation reagents are added to the volume. The ligation reaction yields a volume containing a set of oligonucleotides including components, fragments, and FLIs. In some implementations, following the ligation reaction, the terminal ends are de-protected, e.g., hairpins at the terminal ends of the edge components are removed, e.g., using DNA-dependent protein kinase catalytic subunit (DNA- PKcs) and Artemis (a structure-specific endonuclease). Subsequently, PCR primers are hybridized to the oligonucleotides. The oligonucleotides are then subjected to PCR amplification. Any chimeric component or fragment with a terminal ddATP is not amplified due to the inhibition of DNA polymerase by ddATP, nor can modified components or fragments act as PCR primers. This process increases the signal (FLI) to noise (components, fragments) ratio of the DNA coding/decoding process. The chemical process can be performed in a batch processing method or in a microfluidic device. After PCR amplification, the oligonucleotides can be sequenced and the information encoded therein can be read.

[0293] The technologies described in this specification can be used each alone or in combination with one or more other technologies described in this specification. In some implementations, modified nucleotides that can similarly block PCR extension from unligated products can be used, for example, Acyclonucleotides (or acyclic nucleotides). In acyclonucleotides, a (single) phosphate nucleotide has a bond arrangement between the sugar and phosphate groups that is not cyclic, resulting in the loss of the 3 ’-OH group needed for chain extension. In principle, any modification that results in loss or replacement of the 3 ’-OH group of a nucleotide (e.g., replacement with C3 spacers, e.g., a C3 propyl spacer that can be incorporated internally or at the either end of an oligonucleotide during chemical synthesis, or a phosphate group) can be used for this purpose.

[0294] In an example process, a reaction volume includes a plurality of components of one or more layers. The components include a plurality of edge components. The components have 5’ overhangs. A volume containing a polymerase (e.g., T4 polymerase, Therminator DNA polymerase, TdT) and a volume containing one or more Acyclonucleotides (e.g., acyclic A, C, T, or G) are added. The Acyclonucleotides are added to the 3’ ends of the components by hybridization to the 5’ overhangs. In some implementations, the ends of the edge components that are configured to be the terminal ends of the FLI are modified, e.g., to protect FLIs from the noise reduction processes described below (e.g., using a hairpin loop at the terminal ends). After incubation, the product is purified (e.g., using gel extraction, silica columns, alcohol precipitation, or magnetic SPRI beads) to ensure ddNTPs are not carried over into future reactions. To ligate the components, T4 Ligase, ATP, and/or other appropriate ligation reagents are added to the volume. The ligation reaction yields a volume containing a set of oligonucleotides including components, fragments, and FLIs. In some implementations, following the ligation reaction, the terminal ends are de-protected, e.g., hairpins at the terminal ends of the edge components are removed, e.g., using DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Artemis (a structure-specific endonuclease). Subsequently, PCR primers are hybridized to the oligonucleotides. The oligonucleotides are then subjected to PCR amplification. Any chimeric component or fragment with a terminal Acyclonucleotide is not amplified due to the inhibition of DNA polymerase by Acyclonucleotides, nor can modified components or fragments act as PCR primers. This process increases the signal (FLI) to noise (components, fragments) ratio of the DNA coding/decoding process. The chemical process can be performed in a batch processing method or in a microfluidic device. After PCR amplification, the oligonucleotides can be sequenced and the information encoded therein can be read.

[0295] Other mechanisms of blocking include changes to the structure of a DNA strand to block the activity of DNA polymerase. An example of this is to generate oligonucleotides containing a 3’ flap that can block polymerase translocation and prevent amplification from unligated products (FIG. 21).

[0296] In an example process, a reaction volume includes a plurality of components of one or more layers. The components include a plurality of edge components. The components have 3’ overhangs or 5’ overhangs. In some implementations, the ends of the edge components that are configured to be the terminal ends of the FLI are modified, e.g., to protect FLIs from the noise reduction processes described below (e.g., using a hairpin loop at the terminal ends).

[0297] In some implementations, components are ligated to form identifiers. To ligate the components, T4 Ligase, ATP, and/or other appropriate ligation reagents are added to the volume. The ligation reaction yields a volume containing a set of oligonucleotides including components, fragments, and FLIs. After ligation, a volume containing a polymerase (e.g., T4 polymerase, Therminator DNA polymerase, TdT) and a volume containing one or more single-stranded DNA molecules including a non-hybridizing region (“flaps”) are added. In some implementations, the flaps are added to the 3’ ends of the components by hybridization to the 5’ overhangs. In some implementations, following the ligation reaction, the terminal ends are de-protected, e.g., hairpins at the terminal ends of the edge components are removed, e.g., using DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Artemis (a structure-specific endonuclease).

Subsequently, PCR primers are hybridized to the oligonucleotides. The oligonucleotides are then subjected to PCR amplification. Any chimeric component or fragment with a terminal flap is not amplified due to the inhibition of DNA polymerase by the flap, nor can modified components or fragments act as PCR primers. This process increases the signal (FLI) to noise (components, fragments) ratio of the DNA coding/decoding process. The chemical process can be performed in a batch processing method or in a microfluidic device. After PCR amplification, the oligonucleotides can be sequenced and the information encoded therein can be read.

[0298] Besides their use in improving decodability, the technologies described in this specification provide the capability to “encrypt” DNA encoded information/data by adding in shorter fragments of DNA that encourage recombination. This method can increase noise and prevent decodability under standard processes. Methods of noise reduction, such as treatment with ddNTPs as described in this specification, would thus be required to successfully decode such data. Similarly, large, targeted oligonucleotides containing terminal ddNTPs could be added to samples to competitively block amplification of either the whole dataset or regions downstream of specific sequences, providing a mechanism of decreasing decodability for the purposes of data security.

Nuclease Resistance

[0299] Described in this specification are technologies to reduce noise in decoding information stored in nucleic acids. As discussed above, noise can be caused by the presence of incomplete product of the nucleic acid synthesis process (e.g., assembly of nucleic acid identifiers from two or more components) to encode information in nucleic acid molecules. The removal of shorter fragments in existing workflows involves a subjective, manual process, i.e., gel extraction. With this approach, a large quantity of shorter fragments are removed from samples (but a significant number remains) at the cost of a significant amount of full length product. Moreover, there is a high degree of variability in yield recovery using this method. Therefore, alternatives to this approach, as described in this specification, can be beneficial.

[0300] In some implementations, nucleases can be used. Nucleases are highly active, powerful enzymes that can degrade DNA by cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleic acid molecules, such as identifiers or components thereof, can be modified to provide resistance to nucleases. This specification describes modifications that can be added to edge components that can selectively protect Full-Length Identifiers (FLIs) from nuclease activity, whilst removing unprotected molecules of DNA, e.g., incompletely assembled products (FIG. 22). This process can increase signal-to-noise ratio (SNR.) and the likelihood of successful decodability

[0301] Described in this specification are technologies to prevent FLIs from being destroyed by nucleases. This prevention can be achieved by protecting the edge components of FLIs from nuclease activity. In some implementations, prior to the assembly of the identifier, e.g., as discussed above, the edge components are modified using one or more techniques described below. [0302] In some implementations, the technologies described in this specification include edge components with hairpin loops. As described above, designing edge components that include hairpin loops can result in FLIs being uniquely capped by hairpins, e.g., as illustrated in FIG. 23. These hairpins provide resistance to one or more nucleases, while unprotected molecules are exposed and subjected to cleavage and degradation by a nuclease, leaving behind FLIs.

[0303] In some implementations, the technologies described in this specification include protelomerase based FLI protection. In some implementations, protelomerases can be used to protect the edge components from nuclease activity. Protelomerases are enzymes that cleave at a specific site, resulting in the generation of covalently closed ends as shown in FIG. 24. This method is based on the same principle as the use of hairpin-like modifications that provide nuclease resistance. Protelomerase treatment results in edge components having covalently closed ends providing FLIs with protection from nucleases as illustrated in FIG. 25. In some implementations, protelomerase recognition sequences can be added to edge components following ligation. In some implementations, protelomerase recognition sequences can be added to edge components prior to ligation.

[0304] In some implementations, the technologies described in this specification include phosphorothionate bond based FLI protection. In some implementations, Phosphorothioate (pt) bonds can be used to protect the edge components from nuclease activity. A Phosphorothioate (pt) bond is a phosphodiester linkage where a non-bridging oxygen is replaced by sulfur. The substitution of oxygen with sulfur does not change the reactivity of the bond, but now that the phosphorus is connected to distinct groups it creates a chiral center with 2 possible configurations, “RP” and “SP” (FIG. 26). In certain configurations, the Phosphorothioate (pt) bond results in resistance to specific nucleases. For example, Exonuclease III has been shown to cleave SP but not RP bonds. In some implementations, at least 3 pt bond modifications are incorporated on each end of the FLI. In some implementations, at least 5 pt bond modifications are incorporated on each end of the FLI. In some implementations, at least 2, 3, 4, 5, 10, or more pt bond modifications are incorporated on each end of the FLI. Incorporating at least these numbers of pt bonds ensures a high likelihood that the preferred configuration is present in the target molecule. Similar to the prior modifications, edge components containing multiple phosphorothionate bonds can protect FLIs from nuclease treatment and can be used to remove incompletely assembled products.

[0305] In some implementations, the technologies described in this specification include inverted dT modifications. In some implementations, inverted dTs can be used to protect the edge components from nuclease activity. An inverted dT is a modification of the 3’ end of an oligonucleotide (FIG. 27). This modification creates a 3 ’-3’ linkage that stops DNA polymerase from further extending the DNA sequence. Moreover, this modification confers resistance to nucleases. Designing and implementing identifiers (e.g., edge components) that contain an inverted dT on the terminal ends of identifiers can be a mechanism of enriching for FLIs following nuclease treatment.

[0306] In some implementations, the technologies described in this specification include incorporation of modified sugar residues. In some implementations, modified sugar residues can be used to protect the edge components from nuclease activity (FIG. 28). Similar to the technologies described above, the presence of modified sugar residues on edge components can provide nuclease resistance to FLIs, while incompletely assembled products remain degradable by nucleases. Examples of sugar modifications include modification with ribose, 2’- Methoxy, and 2’- Methoxy ethyl.

[0307] In some implementations, the technologies described in this specification include circularization of identifiers. In some implementations, circularization of the identifier molecule can be used to protect the edge components from nuclease activity once the identifier is fully ligated. This technology includes designing and implementing overhangs on edge components that enable FLI’s to circularize on themselves and/or generating unique overhangs that enable FLIs to ligate to a DNA backbone. Nucleases that breakdown linear DNA can be used to remove incompletely assembled fragments from the samples. This approach can be carried out either during ligation of components or can be modified to provide circularization during postprocessing. The latter approach includes designing and implementing restriction enzyme sites on edge components. Ligation blunting (e.g., using nucleases) can be used to remove overhangs from incompletely assembled fragments (to prevent promiscuous ligation). Thereafter, restriction enzyme digestion can generate overhangs that enable the circularization of FLIs (following a ligation reaction), thereby protecting the edge components from nuclease activity.

[0308] In some implementations, the technologies described in this specification include helicase-based targeted removal of incompletely assembled fragments. In some implementations, helicase can be used for removal of incompletely assembled fragments. Helicases are proteins that move directionally along a nucleic acid phosphodiester backbone, separating two hybridized nucleic acid strands. This technology includes targeting the overhangs that are uniquely present on incompletely assembled products by utilizing helicases that target overhangs. These helicases can specifically unwind DNA containing overhangs providing access to nucleases that act on single stranded DNA. FLI lacking overhangs (e.g., due to blunt ends or circularization) lack overhangs and are therefore protected.

Example Implementations

[0309] Item 1. A method for writing information into a nucleic acid molecule with reduced noise, the method comprising: determining a string of symbols to represent said information and generating a plurality of oligonucleotides comprising a plurality of identifiers, wherein an individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols, wherein generating the plurality of oligonucleotides comprises: (a) constructing a plurality of components, wherein each individual component of said plurality of oligonucleotides is a nucleic acid molecule having a nucleic acid sequence, a 3’-end, and a 5’- end; (b) adding, to a reaction volume comprising the plurality of components, a first volume comprising a template-independent polymerase and an amount of dideoxynucleotides (ddNTPs);

(c) incubating the reaction volume to attach a ddNTP to the 3 ’-ends of at least a portion of the components; (d) adding, to the reaction volume, a reagent to chemically link together two or more components of said plurality of components, thereby generating the plurality of identifiers and a plurality of fragments; and (e) adding, to the reaction volume, PCR primers and subsequently performing PCR amplification, wherein PCR amplification of any oligonucleotide comprising a ddNTP is inhibited.

[0310] Item 2. The method of item 1, wherein the plurality of components comprises a plurality of edge components, each edge component having a terminal end, and each edge component being configured such that the terminal end of the edge component constitutes a terminal end of an identifier.

[0311] Item 3. The method as in any one of items 1-2, wherein the first volume comprises deoxynucleotides (dNTP).

[0312] Item 4. The method as in any one of items 1-3, wherein the polymerase comprises terminal transferase (TdT) that catalyzes the addition of nucleotides to the 3 ’-ends of the plurality of the components.

[0313] Item 5. The method of as in any one of items 1-4, wherein the 3 ’-ends of the plurality of the components comprise 3 ’-end overhangs.

[0314] Item 6. The method as in any one of items 1-5, wherein the ddNTP is one or more of ddATP, ddGTP, ddTTP, or ddCTP.

[0315] Item 7. The method as in any one of items 1-6, wherein the polymerase comprises T4 polymerase or Therminator DNA polymerase.

[0316] Item 8. The method as in any one of items 1-7, comprising forming 5’-end overhangs on the plurality of the components. [0317] Item 9. The method as in any one of items 1-8, comprising removing overhangs from the 3’-end and/or the 5’-end of the plurality of the components prior to the attachment of the ddNTP molecules.

[0318] Item 10. The method of item 9, wherein the overhangs are removed using a nuclease.

[0319] Item 11. The method of item 10, wherein the nuclease includes one or more of Mung

Bean nuclease, Nuclease Pl, Exonuclease I, Exonuclease III, Micrococcal Nuclease, SI Nuclease, or polymerases that contain exonuclease activity.

[0320] Item 12. The method as in any one of items 1-11, wherein the attachment of the ddNTP molecules comprises adding ddATP on the 3 ’-end of the components using a polymerase. [0321] Item 13. The method of item 12, wherein the polymerase comprises taq polymerase or Klenow fragments.

[0322] Item 14. A method for writing information into a nucleic acid molecule, the method comprising: determining a string of symbols to represent said information and generating a plurality of oligonucleotides comprising a plurality of identifiers, wherein an individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols, wherein generating the plurality of oligonucleotides comprises: (a) constructing a plurality of components, wherein each individual component of said plurality of oligonucleotides is a nucleic acid molecule having a nucleic acid sequence, a 3 ’-end, and a 5 ’-end; (b) adding, to a reaction volume comprising the plurality of components, a first volume comprising a polymerase and an amount of acyclonucleotides; (c) incubating the reaction volume to attach an acyclonucleotide to the 3 ’-ends of at least a portion of the components; (d) adding, to the reaction volume, a reagent to chemically link together two or more components of said plurality of components, thereby generating the plurality of identifiers and a plurality of fragments; and (e) adding, to the reaction volume, PCR primers and subsequently perform PCR amplification, wherein PCR amplification of any oligonucleotide comprising an acyclonucleotides is inhibited. [0323] Item 15. A method for writing information into a nucleic acid molecule, the method comprising: determining a string of symbols to represent said information and generating a plurality of oligonucleotides comprising a plurality of identifiers, wherein an individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols, wherein generating the plurality of oligonucleotides comprises: (a) constructing a plurality of components, wherein each individual component of said plurality of oligonucleotides is a nucleic acid molecule having a nucleic acid sequence, a 3 ’-end, and a 5 ’-end; (b) adding, to the reaction volume, a reagent to chemically link together two or more components of said plurality of components, thereby generating the plurality of identifiers and a plurality of fragments; (c) adding, to a reaction volume comprising the plurality of components, a first volume comprising a polymerase and a plurality of 3’-DNA flaps; (d) incubating the reaction volume to attach a 3’- DNA flap to the 3 ’-ends of at least a portion of the components and fragments; and (e) adding, to the reaction volume, PCR primers and subsequently performing PCR amplification, wherein PCR amplification of any oligonucleotide comprising a 3’-DNA flap is inhibited.

[0324] Item 16. A method for writing information into a nucleic acid molecule, comprising: (a) determining a string of symbols to represent said information; (b) constructing a plurality of components, wherein each individual component of said plurality of components is a nucleic acid molecule having a nucleic acid sequence, a 3 ’-end, and a 5 ’-end; (c) chemically linking together two or more components of said plurality of components thereby generating a plurality of identifiers, wherein each identifier of said plurality of identifiers comprises two or more components, each identifier having a first end and a second end, each component disposed at the first end of the identifier being a first edge component, and each component disposed at the second end of the identifier being a second edge component; and (d) chemically modifying terminal ends of each of the first edge component, the second edge component, or both, such that first edge component and/or the second edge components are protected from exonuclease activity. wherein an individual identifier of said plurality of identifiers corresponds to an individual symbol in said string of symbols.

[0325] Item 17. The method of item 16, wherein modifying the terminal ends comprises constructing hairpin loop at one or both of said terminal ends, thereby protecting the one or both terminal ends from nuclease activity.

[0326] Item 18. The method as in any one of items 16-17, wherein modifying the terminal ends comprises attaching a protelomerase recognition sequence at one or both of said terminal ends to covalently close said one or both terminal ends, thereby protecting the one or both terminal ends from nuclease activity.

[0327] Item 19. The method as in any one of items 16-18, wherein modifying the terminal ends comprises implementing a phosphorothionate bond at one or both of said terminal ends to substitute a sulfur atom for a non-bridging oxygen in the phosphate backbone of a terminal oligonucleotide, thereby protecting the one or both terminal ends from nuclease activity.

[0328] Item 20. The method of item 19, wherein modifying the terminal ends comprises implementing multiple phosphorothionate bonds at one or both of said terminal ends.

[0329] Item 21. The method of item 20, wherein modifying the terminal ends comprises implementing at least three phosphorothionate bonds at one or both of said terminal ends [0330] Item 22. The method as in any one of items 16-21, wherein modifying the terminal ends comprises implementing an inverted dT modification at one or both of said terminal ends to create a 3 ’-3’ linkage, thereby protecting the one or both terminal ends from nuclease activity.

[0331] Item 23. The method as in any one of items 16-22, wherein modifying the terminal ends comprises implementing an sugar residue modification at one or both of said terminal ends, thereby protecting the one or both terminal ends from nuclease activity.

[0332] Item 24. The method as in any one of items 16-23, wherein modifying the terminal ends comprises circularizing the identifiers and joining said terminal ends, thereby protecting the one or both terminal ends from nuclease activity.

-I l l- [0333] Item 25. The method as in any one of items 16-24, wherein modifying the terminal ends comprises modifying the terminal ends with restriction enzyme sites.

[0334] Item 26. The method as in any one of items 1-25, comprising targeting overhangs that are uniquely present on incompletely assembled identifiers by utilizing a helicase to separate two hybridized nucleic acid strands, thereby providing access to nucleases that act on single stranded DNA.

[0335] Item 27. The method as in any one of items 1-26, comprising treating the components with an exonuclease.

[0336] Item 28. The method as in any one of items 1-27, comprising,

[0337] selectively capturing or amplifying an identifier library comprising at least a subset of said plurality of identifiers.

[0338] Item 29. The method as in any one of items 1-28, wherein each symbol of said string of symbols is one of one or more possible symbol values.

[0339] Item 30. The method of item 29, wherein each symbol in said string of symbols is one of two possible symbol values.

[0340] Item 31. The method as in any one of items 29-30, wherein one symbol value at each position of said string of symbols may be represented by the absence of a distinct identifier in the identifier library.

[0341] Item 32. The method of item 30, wherein said two possible symbol values are a bitvalue of 0 and 1, wherein said individual symbol with said bit-value of 0 in said string of symbols may be represented by an absence of a distinct identifier in said identifier library, wherein said individual symbol with said bit-value of 1 in said string of symbols may be represented by a presence of said distinct identifier in said identifier library, or vice versa.

[0342] Item 33. The method as in any one of items 1-32, comprising chemically linking said two or more components from two or more layers and wherein each layer of said two or more layers comprises a distinct set of components. [0343] Item 34. The method of item 33, wherein said individual identifier from said identifier library comprises one component from each layer of said two or more layers.

[0344] Item 35. The method of item 34, wherein said two or more components are assembled in a fixed order.

[0345] Item 36. The method of item 34, wherein said two or more components are assembled in any order.

[0346] Item 37. The method of item 34, wherein said two or more components are assembled with one or more partitioning components disposed between two components from different layers of said two or more layers.

[0347] Item 38. The method of item 33, wherein said individual identifier comprises one component from each layer of a subset of said two or more layers.

[0348] Item 39. The method of item 33, wherein said individual identifier comprises at least one component from each of said two or more layers.

[0349] Item 40. The method as in any one of items 1-39, comprising using an endonuclease to generate at least one sticky end of an individual component of said plurality of components.

[0350] Item 41. The method of item 40, wherein said at least one sticky end is at a 5' end of said individual component.

[0351] Item 42. The method of item 40, wherein said at least one sticky end is at a 3 ’-end of said individual component.

[0352] Item 43. The method as in any one of items 40-42, comprising generating two sticky ends of said individual component.

[0353] Item 44. The method as in any one of items 40-43, wherein said at least one sticky end is at least one nucleotide in length.

[0354] Item 45. The method as in any one of items 40-44, wherein said at least one sticky end is six nucleotides in length. [0355] Item 46. The method as in any one of items 1-45, wherein said plurality of identifiers comprises nucleic acid sequences that store metadata of said information or conceals said information.

[0356] Item 47. The method as in any one of items 1-46, wherein two or more identifier libraries are combined and wherein each identifier library of said two or more identifier libraries is tagged with a distinct barcode.

[0357] Item 48. The method as in any one of items 28-47, wherein each individual identifier in said identifier library comprises a distinct barcode.

[0358] Item 49. The method as in any one of items 1-48, wherein said plurality of identifiers, or said plurality of components that comprise said identifiers, is selected for ease of read, write, access, copy, and deletion operations.

[0359] Item 50. The method as in any one of items 1-49, wherein chemically linking comprises ligating together two or more components of said plurality of components using a reagent comprising a ligase.

[0360] Item 51. The method of item 50, wherein said ligase is a T4 ligase, a T7 ligase, a T3 ligase, or an E coli ligase.

[0361] Item 52. The method as in any one of items 50-51, wherein said reagent further comprises an additive.

[0362] Item 53. The method of item 52, wherein said additive increases efficiency of said ligase.

[0363] Item 54. The method as in any one of items 52-53, wherein said additive comprises polyethylene glycol (PEG).

[0364] Item 55. The method of item 54, wherein said PEG is PEG400, PEG6000, PEG8000 or any combination thereof.

[0365] Item 56. The method as in any one of items 50-55, wherein a reaction time of said ligating is at least one minute. [0366] Item 57. The method as in any one of items 50-55, wherein said ligating is at 30 degrees Celsius or higher.

[0367] Item 58. The method as in any one of items 50-57, further comprising inactivating said ligase using a buffer containing EDTA or guanidine thiocyanate.

[0368] Item 59. The method as in any one of items 50-58, wherein final concentration of said ligase is at least about 5 CEU/p L.

[0369] Item 60. The method as in any one of items 50-59, wherein said reagent further comprises glycerol molecules.

[0370] Item 61. The method as in any one of items 1-60, wherein the chemically linking comprises using overlap-extension polymerase chain reaction (PCR).

[0371] Item 62. The method as in any one of items 1-61, wherein said individual component is a deoxyribonucleic acid (DNA) or a ribonucleic acid.

[0372] Item 63. The method as in any one of items 1-62, wherein said individual component has been rehydrated.

[0373] Item 64. The method as in any one of items 1-63, wherein said individual component is rehydrated from a dehydrated component.

[0374] Item 65. The method as in any one of items 28-64, further comprising dehydrating said identifier library by dehydrating each individual identifier of at least said subset of said plurality of identifiers.

[0375] Item 66. The method as in any one of items 28-65, wherein each individual identifier of at least said subset of said plurality of identifiers is dehydrated.

[0376] Item 67. The method as in any one of items 65-66, further comprising rehydrating each individual identifier of at least said subset of said plurality of identifiers.

[0377] Item 68. The method as in any one of items 1-67, further comprising adding a preserving additive to the identifier library to prevent identifier degradation. [0378] Item 69. The method as in any one of items 1-68, wherein said plurality of identifiers is copied with PCR.

[0379] Item 70. The method of item 69, wherein said PCR has at least 10 cycles

[0380] Item 71. The method of item 69, wherein said plurality of identifiers is amplified with PCR up to a concentration 10 nanograms per microliter.

[0381] Item 72. The method as in any one of items 69-71, wherein said PCR is an emulsion PCR.

[0382] Item 73. The method as in any one of items 1-72, wherein said plurality of identifiers is copied with linear amplification.

[0383] Item 74. The method as in any one of items 69-73, wherein after said PCR, linear amplification is used to create more copies of said plurality of identifiers.

[0384] Item 75. The method as in any one of items 1-74, wherein a subset of said plurality of identifiers is accessed with one or more PCR reactions.

[0385] Item 76. The method as in any one of items 1-75, wherein a subset of said plurality of identifiers is accessed with one or more affinity tagged probes.

[0386] Item 77. The method as in any one of items 75-76, wherein identifiers of said subset of said plurality of identifiers have a set of components in common.

[0387] Item 78. The method as in any one of items 1-77, wherein said identifiers are purified by gel electrophoresis.

[0388] Item 79. The method as in any one of items 1-78, wherein said identifiers are purified by affinity tagged probes.

[0389] Item 80. The method as in any one of items 1-79, wherein said identifiers are amplified using PCR.

[0390] Item 81. The method as in any one of items 1-80, where said identifiers are designed to avoid thymine-thymine dinucleotides or cytosine-cytosine dinucleotides.