[0001] Colorimetric Detection of Nucleic Acid Amplification RELATED APPLICATIONS

[0002] This application claims the benefit of U.S. provisional application 61/983,687, filed April 24, 2014, the disclosure of which is hereby incorporated by reference.

SEQUENCE LISTING

[0003] The instant application contains a Sequence Listing which has been filed

electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on April 14, 2015, is named 28770PCT_CRF_sequencelisting.txt and is 5,524 bytes in size.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

[0004] This invention was made with government support awarded by the Small Business Innovation Research Program at the National Institutes of Health (Grant No. 1R41AI114068- 01). The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Field of the invention

[0005] The invention relates to methods and compositions for colorimetric detection of nucleic acid amplification reaction products. In particular, the invention relates to accelerated colorimetric detection of nucleic acid amplification reaction products, using a reaction mix including one or more halochromic agents.

Description of the Related Art

[0006] Some current methods for the detection of specific nucleic acid sequences and nucleic acid biomarkers involve fluorescence methods. DNA primers are designed to amplify nucleic acid sequences from a sample using nucleic acid amplification schemes such as PCR

(polymerase chain reaction) and LAMP (loop-mediated amplification). Typically, the resulting amplicons are detected and quantified through fluorescence techniques using an intercalating fluorophore or molecular probe. However, these techniques require

sophisticated instrumentation, including optical components, an excitation source, and one or more sensors for detection of the fluorescent emission. These instruments are potentially large, cumbersome, and expensive. Alternatively, the amplicons can be colorimetrically visualized using agarose gels or lateral flow assays. However, these techniques require additional steps, which increase the time to result, and in some cases need instrumentation such as a gel box.

SUMMARY OF THE INVENTION

[0007] Disclosed herein are methods and kits for colorimetric detection of an amplification reaction product. The methods include contacting the sample with a reaction mix under conditions such that an amplification reaction occurs and produces an amplification reaction product if the sample contains a target nucleic acid template molecule. The reaction mix includes an enzyme for catalyzing the amplification reaction, and a halochromic agent. In some embodiments, the reaction mix includes more than one halochromic agent. In some embodiments, the reaction mix also includes a buffer having a buffering capacity equivalent to Tris buffer at a concentration between 1 mM-19 mM in a solution having a starting pH of 8.0. If the target nucleic acid template molecule is present, the amplification reaction changes the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating the presence of the target nucleic acid. In some embodiments, the detectable colorimetric change is quantified at a cell path length of 50 μιη. If the target nucleic acid template molecule is not present, the amplification reaction does not generate an adequate number of protons to sufficiently change the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating that the amplification reaction product has not been produced.

[0008] The kit includes an enzyme for catalyzing an amplification reaction, a halochromic agent, and optionally a buffer having a buffering capacity equivalent to Tris buffer at a concentration between 1 mM-19 mM in a solution having a starting pH of 8.0. The kit further includes instructions for use comprising instructions for contacting a sample with a reaction mix including the buffer and the enzyme and the halochromic agent under conditions that an amplification reaction occurs and produces an amplification reaction product if the sample contains a target nucleic acid template molecule, the reaction mix having a starting pH. If the target nucleic acid template molecule is present, the amplification reaction changes the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating the presence of the target nucleic acid. If the target nucleic acid template molecule is not present, the amplification reaction does not generate an adequate number of protons to sufficiently change the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating that the amplification reaction product has not been produced. BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

[0009] These and other features, aspects, and advantages of the present invention will become better understood with regard to the following description, and accompanying drawings, where:

[0010] FIG. 1 shows the DNA sequence of a template nucleic acid molecule target region from Schistosoma mansoni (SEQ ID NO: 23), according to an embodiment.

[0011] FIG. 2 is a graph indicating pH measurements for positive and negative isothermal amplification reactions, according to an embodiment.

[0012] FIG. 3 is a graph showing the detection of color (hue) of positive and negative isothermal amplification reactions at the reaction endpoints, according to an embodiment.

[0013] FIG. 4 shows the results of a gel electrophoresis assay of positive and negative isothermal amplification reaction products, according to an embodiment.

[0014] FIG. 5 shows the normalized hue values for amplification reactions using various Tris buffer concentrations, according to an embodiment.

[0015] FIG. 6 shows the normalized hue values for amplification reactions using varying amounts of additional hydronium ion equivalents, according to an embodiment.

[0016] FIGs. 7A, 7B, 7C, and 7D show the normalized hue values for amplification reactions using various halochromic agent concentrations, according to an embodiment.

[0017] FIG. 8 shows the compatibility of different polymerases with visual detection of LAMP amplification, according to an embodiment.

[0018] FIGs. 9 A and 9B show the normalized hue values for amplification reactions using varying channel depths, according to an embodiment.

[0019] FIG. 10 shows the normalized hue values over time for SDA, according to an embodiment.

[0020] FIG. 11 shows the normalized hue values over time for PCR, according to an embodiment.

[0021] FIGs. 12A and 12B show the normalized contrast changes for amplification reactions using combinations of halochromic agents, according to an embodiment.

[0022] FIG. 13 shows the normalized contrast changes over time for different DNA template concentrations, according to an embodiment.

DETAILED DESCRIPTION OF THE INVENTION

[0023] Disclosed herein are compositions and methods for colorimetric detection of nucleic acid amplification reaction products. In some embodiments, amplified reaction products are detected by a visual color change observation or by measuring absorbance or fluorescence of the color change of a halochromic agent in the amplification reaction mix.

Definitions

[0024] Terms used in the claims and specification are defined as set forth below unless otherwise specified.

[0025] The term "colorimetry" or "colorimetric" refers to techniques of quantifying or otherwise observing colored compound concentrations in solution. "Colorimetric detection" refers to any method of detecting such colored compounds and/or the change in color of the compounds in solution. Methods may include visual observation, absorbance measurements, or fluorescence measurements, among others.

[0026] The term "halochromic agent" refers to a composition that changes color upon some chemical reaction. In particular, a halochromic agent can refer to a composition that changes color with a pH change. Different halochromic agents may change colors over different pH transition ranges.

[0027] The term "transition pH range" or "pH transition range" refers to a pH range over which the color of a particular sample or compound changes. A specific transition pH range for a sample may depend on a halochromic agent in the sample (see above).

[0028] The term "nucleic acid amplification" or "amplification reaction" refers to methods of amplifying DNA, RNA, or modified versions thereof. Nucleic acid amplification includes several techniques, such as an isothermal reaction or a thermocycled reaction. More specifically, nucleic acid amplification includes methods such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), strand displacement amplification (SDA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), multiple displacement amplification (MDA), rolling circle amplification (RCA), and nucleic acid sequence-based amplification (NASBA). The term "isothermal amplification" refers to an amplification method that is performed without changing the temperature of the amplification reaction. Protons are released during an amplification reaction: for every deoxynucleotide triphosphate (dNTP) that is added to a single-stranded DNA template during an amplification reaction, one proton (H ⁺ ) is released.

[0029] The term "sufficient amount" means an amount sufficient to produce a desired effect, e.g., an amount sufficient to modulate protein aggregation in a cell.

[0030] The term percent "identity," in the context of two or more nucleic acid or polypeptide sequences, refer to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection. Depending on the application, the percent "identity" can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.

[0031] For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

[0032] Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally Ausubel et al, infra).

[0033] One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al, J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information

(www.ncbi.nlm.nih.gov ).

[0034] It must be noted that, as used in the specification and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise.

Compositions of the invention

[0035] Disclosed herein are compositions and methods for accelerated and efficient colorimetric detection of nucleic acid amplification reaction products. In an embodiment, a colorimetric assay is used to visually detect the presence of an amplified nucleic acid product, which eliminates the need for expensive and sophisticated instrumentation. [0036] In some embodiments, the colorimetric detection of amplification products is achieved by amplifying a target nucleic acid template molecule to obtain the amplification reaction product. The amplification reaction includes a reaction mix. In an embodiment, the reaction mix includes a nucleic acid template molecule, one or more enzymes for catalyzing the amplification reaction, and one or more halochromic agents for colorimetric detection. In a further embodiment, the reaction mix also includes a buffer having a buffering capacity equivalent to Tris buffer at a concentration between 1 mM-19 mM in a solution having a starting pH of 8.0. In further embodiments, the reaction mix also includes a plurality of nucleic acid primers, deoxynucleotide triphosphates (dNTPs), suitable salts for the enzyme, and other non-buffered chemicals that enable nucleic acid amplification.

[0037] During the amplification reaction, one proton is released for each dNTP that is incorporated into a nucleic acid template molecule. Thus, the pH of the reaction mix decreases throughout the amplification reaction. In an embodiment, if the target nucleic acid is present, the amplification reaction changes the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating the presence of the target nucleic acid, and if the target nucleic acid is not present, the amplification reaction does not generate a sufficient number of protons to change the starting pH of the reaction mix sufficient to cause a detectable colorimetric change of the halochromic agent, thereby indicating that the amplification reaction product has not been produced. In an embodiment, the halochromic agent (or pH indicator) in the reaction mix has a transition pH range for a colorimetric change of the halochromic agent that is narrower than an expected pH change between (1) a starting pH of the reaction mix before the amplification reaction is performed, and (2) an ending pH of the reaction mix after the amplification reaction has been performed.

[0038] In an embodiment, the halochromic agent is a colorimetric agent or a fluorescent agent. Suitable halochromic agents include phenol red, bromocresol purple, bromothymol blue, neutral red, naphtholphthalein, cresol red, cresolphthalein, phenolphthalein, methyl red, and thymolphthalein, among others. A wide range of concentrations of these halochromic agents can be used in the reaction mix. Different halochromic agents have different transition pH ranges. In some embodiments, the halochromic agent has a transition pH range between pH 5-10, between pH 6-9, or between pH 6.5-8.8. In another embodiment, the halochromic agent is at a concentration between 25-100 μΜ in the reaction mix. In another embodiment, the halochromic agent is at a concentration between 50-260 μΜ. In some embodiments, a combination of two or more halochromic agents is used in the reaction mix, which increases the normalized color contrast change of the reaction mix by being of complementary colors at the beginning and similar colors at the end of the amplification reaction. In a further embodiment, the combination of halochromic agents comprises phenol red and bromothymol blue. In a further embodiment, the combination of halochromic agents comprises cresol red and bromothymol blue.

[0039] In one example, Phenol red is a halochromic agent that has a transition pH range from around 6.4-8.0. At the upper limit of the transition pH range, phenol red is red, and at the lower limit of the transition pH range, phenol red is yellow. A reaction mix containing phenol red will change color from red to yellow throughout the amplification reaction, as long as the starting pH of the reaction mix is around or above 8.0, and the ending pH of the reaction mix is within the transition pH range or around or below 6.4.

[0040] In some embodiments, the starting pH of the reaction mix is set by adding an acid or a base to the reaction mix until the desired starting pH is reached. The ending pH of the reaction mix is determined by performing a sample amplification reaction and measuring the ending pH (for example, with a micro-pH electrode). In an embodiment, the halochromic agent for an amplification reaction is selected so that the transition pH range lies in between the starting pH and ending pH. In a further embodiment, the halochromic agent is selected so that the transition pH range is nearer to the starting pH than the ending pH. The halochromic agent can also be selected based on the particular enzyme used for catalyzing the

amplification reaction. Near the ending pH, the enzyme in the reaction mix terminates polymerization of the amplification reaction as the pH decreases to unfavorable H ⁺ concentrations. In an embodiment, additional hydronium ions or hydronium ion equivalents are added to the reaction mix via the sample. For example, between 4.8 x 10 ^"9 and 4.8 x 10 ^"18 additional hydronium ion equivalents per 10 μΐ reaction mix can be tolerated for the amplification reaction to proceed. In a further embodiment, between 4.8 x 10 ^"10 and 4.8 x 10 ^{" 18} , 4.8 x 10 ^"12 and 4.8 x 10 ^"18 , or 4.8 x 10 ^"15 and 4.8 x 10 ^"18 can be tolerated.

[0041] Generally, the enzyme will catalyze amplification reactions within a pH range that encompasses or is close to the transition pH range of the selected halochromic agent. Various enzymes can be used for the reaction, and different enzymes catalyze amplification reactions at different pH ranges. For example, Bst polymerase is believed to catalyze amplification reactions within the pH range of 6.6-9.0. The preferred starting pH for Bst polymerase is greater than 7, more preferably greater than 8.2, and more preferably at 8.8. Other examples of a preferred starting pH for Bst polymerase are found in U.S. Pat. No. 5,830,714, filed April 17, 1996, hereby incorporated by reference in its entirety. In an embodiment, phenol red is coupled with Bst polymerase in a reaction mix, since the pH range at which Bst polymerase is active (6.6-9.0) encompasses the transition pH range of phenol red (6.4-8.0). In another embodiment, methyl red is coupled with U exo-Klenow fragment (polymerase for Helicase Dependent Amplification, HDA) in a reaction mix, since a starting pH at which U exo- Klenow fragment is active (around 7.5) is higher than the transition pH range of methyl red (4.8-6.2).

[0042] Other than Bst or Bst 2.0 polymerase, other enzymes capable of being used for catalyzing the amplification reaction include the polymerase from Thermus aquaticus (TAQ), DNA polymerases I-IV, Kapa Polymerase, R A polymerases I-V, T7 R A Polymerase, a reverse transcriptase, any DNA polymerase or RNA polymerase, a helicase, a recombinase, a ligase, a restriction endonuclease, and a single-strand binding protein. In some embodiments, an isothermal amplification reaction uses an enzyme that is a strand displacement

polymerase, such as phi29-DNA-Polymerase, Klenow DNA-Polymerase, Vent DNA

Polymerase, Deep Vent DNA Polymerase, Bst DNA Polymerase, 9oNm(TM) DNA

Polymerase, U exo-Klenow fragment, or mutants and variants thereof. In some embodiments, suitable salts for the enzyme are also added to the reaction mix. In certain embodiments, the starting pH of the reaction mix is set based on an optimal pH for the specific enzyme used for catalyzing the amplification reaction. In an embodiment, the pH of the entire DNA sample is between pH 3 and pH 11.

[0043] In other embodiments, a fluorescent halochromic agent is used to detect protons released during amplification. The halochromic agent may change optical properties (such as amplitude and emitted wavelength) as the pH of the reaction mix changes during the amplification reaction. Fluorescent halochromic agents include fluorescein, pyranine, and pHrodo dye (Life Technologies, Carlsbad CA).

[0044] The base and/or acid added to the reaction mix maintains the starting pH of the reaction mix around or above an upper limit of the transition pH range of the halochromic agent. For example, an acid such as hydrochloric acid (HC1) or sulfuric acid (H ₂ S0 ₄ ), or a base such as sodium hydroxide (NaOH) or potassium hydroxide (KOH), can be added to the reaction mix. In some embodiments, the acid or base sets the starting pH of the reaction mix between pH 6-10, between pH 7-8, or between pH 8-8.6. In an embodiment, the reaction mix is capable of offsetting the starting pH of the reaction mix by less than 0.1 pH units. In another embodiment, the reaction mix has a starting pH lower than 2 pH units above the upper limit of the transition pH range of the halochromic agent. In further embodiments, the reaction mix has a starting pH lower than 1 pH unit, 0.5 pH units, or 0.1 pH units above the upper limit of the transition pH range of the halochromic agent. In a further embodiment, noise from non-specific amplification is minimized by setting the pH transition range sufficiently separated from the starting pH of the reaction mix, so that any color change is only achieved by a specific and sustained amplification.

[0045] In an embodiment, the reaction mix does not require any additional buffering agent for the amplification reaction, since a buffering agent could prevent large changes in pH from occurring during the amplification reaction. In another embodiment, the reaction mix contains a minimal amount of buffering agent, such that the buffering capacity of the reaction mixture is less than the expected change in pH during amplification. In some embodiments, the buffer is at a concentration between 1 mM and 3 mM. In a further embodiment, the buffer is at a concentration of 1 mM. In certain embodiments, the buffer used is Tris buffer

(formulated to pH 8.8), HEPES (pH 7-9), or TAPS (pH 7-9). In another embodiment, the buffer used is a buffer having a buffering capacity equivalent to a Tris buffer at a

concentration between 1 mM-19 mM in a solution having a starting pH of 8.0. This broad range of suitable buffer concentrations allows the reaction mix to resist unwanted starting pH changes during reaction setup, unlike reaction setups with minimal (<lmM) Tris buffer equivalents (see US 13/799,995, filed March 13, 2013). These unwanted changes in pH come about due to hydronium or hydroxide ion equivalents added to the reaction via the sample reagents. As colorimetric detection and enzyme kinetics depend on the starting pH, the presence of buffer capacity in the reaction mix high enough to avoid starting pH change, but low enough to allow color change upon amplification, become important. In a further embodiment, the pH of the reaction mix is between pH 7.5-8.8. Table 1 shows various buffers having buffering capacities equivalent to a Tris buffer at a concentration between 1 mM-19 mM in a solution having a starting pH of 8.0. The buffer capacity (β) is defined as the equivalents of acid or base needed to change the pH of 1 Liter of buffer by 1 pH unit. This can be calculated as: β = 2.3* C * (Κ^ ΙΉ,Ο^ Κ» + [H ₃ 0 ⁺ ]) ² ); where C is the buffer concentration, K _a is the dissociation constant for the buffer and [H ₃ 0 ] is the hydronium ion concentration of the buffer (which is calculated from the reaction starting pH). The buffer capacity of 1 mM - 19 mM Tris (in a solution having a starting pH of 8.0) was found to range from 0.000575 to 0.010873. The starting pH of the buffer was considered to be in the range of 7.5 - 8.8 to be compatible with the reaction biochemistry (polymerase function, nucleic acid melting, etc.). In other embodiments, the buffer has a buffering capacity equivalent to a Tris buffer at a concentration between 1.5 mM - 19 mM, 2 mM - 19 mM, 3 mM - 19 mM, 4 mM - 19 mM, 5 mM - 19 mM, 6 mM - 19 mM, 7 mM - 19 mM, or otherwise, in a solution having a starting pH of 8.0. In other embodiments, the buffer has a buffering capacity equivalent to a Tris buffer at a concentration between 1.92 mM - 36.29 mM, 3 mM - 36.29 mM, 4 mM - 36.29 mM, 5 mM - 36.29 mM, or otherwise, in a solution having a starting pH of 8.8. In other embodiments, the buffer has a buffering capacity equivalent to a Tris buffer at a concentration between 1.48 mM - 27.92 mM, 2 mM - 27.92 mM, 3 mM - 27.92 mM, 4 mM - 27.92 mM, 5 mM - 27.92 mM, or otherwise, in a solution having a starting pH of 7.5. Table 1: Buffer Capacity Table

8.8 16.28 300.00 ssc Saline Sodium Citrate 7.0 8.0 3.03 57.20

7.5 1.37 25.90

[0046] In an embodiment, a magnesium compound is added to the reaction mix, because magnesium promotes nucleotide incorporation into the template and influences the activity of the polymerase. In a further embodiment, the concentration of a magnesium compound (such as magnesium sulfate) in the reaction mix is at least 0.5 mM, at least 1 mM, at least 2 mM, or at least 4 mM. In an embodiment, the concentration of added magnesium ion is dependent on the concentration of dNTPs, nucleic acid template, and primers. In an embodiment, the ratio of dNTPs to magnesium sulphate in the reaction mix is less than 1 :2, less than 1 :3, less than 1 :4 or less than 1 :5.

[0047] In some embodiments, monovalent cations are added to the reaction mix. Monovalent cations include potassium, ammonium, and quaternary ammonium, among others.

Monovalent cations can affect the melting characteristics of the nucleic acid template and improve the efficiency of the enzyme. In an embodiment, potassium is in the reaction mix at a concentration of less than 50 mM, or less than 15 mM. In another embodiment, quaternary ammonium salts are in the reaction mix at a concentration of greater than 2mM, greater than 5mM, or greater than 8mM. In another embodiment, an ammonium compound (such as ammonium chloride) is in the reaction mix at a concentration of less than 15mM, or less than 10 mM. Ammonium (NH ₄ ⁺ ) has some buffering capability, thus the final concentration of ammonium compounds in the reaction mix should be minimized while maintaining optimal amplification yield.

[0048] In an embodiment, the concentrations of other reagents of the reaction mix are kept at amounts as generally used in amplification reactions. See Notomi T et. al. Nucleic Acids Res. 2000 Jun 15; 28(12): E63; Nature Protocols 2008, Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products, 2008 3(5): pg 880, hereby incorporated by reference in its entirety. In an embodiment, the Bst or Bst 2.0 enzyme is used, and the amount of enzyme is at least 0.8 Unit per microliter of combined fluid. In this embodiment, Betaine is also present in the reaction mix at a concentration between 0-1.5 M or 0.8M-1 M, and the total concentration of primers is between 3.6μΜ and 6.2μΜ. In some embodiments, any of the following reagents is present in the reaction mix: Tris buffer (pH 8.8) at 20 mM, KC1 at 10 mM, MgS0 ₄ at 8 mM, (NH ₄ ) ₂ S0 ₄ at 10 mM,

Tween 20 at 0.1%, Betaine at 0.8 M, dNTPs at 1.4 mM each, MnCl ₂ at 0.5 mM, FIP at 1.6 μΜ, F3 at 0.2 μΜ, B3 at 0.2 μΜ, primers at a total concentration of 5.2 μΜ

(2*(1.6+0.8+0.2), and Bst / Bst 2.0 at 8 U per lOpL.

[0049] The above reagent concentrations have been found to provide good amplification yield and low buffering capacity so that a halochromic pH sensor can be used to detect protons released during the amplification reaction. In some embodiments, the concentrations of reaction mix reagents depend on the enzyme selection. In further embodiments, guidance regarding appropriate reagent concentrations is available from the enzyme manufacturers. In an embodiment, the ratio of the sample volume to the reaction mix volume is such that the sample is diluted between 5% and 40% when the reaction mix is added.

[0050] In some embodiments, amplification reaction reagents are stored separately before being added to a reaction mix, since some reagents have specific required conditions for stability. For example, the enzyme may be stored long term in a moderately buffered solution separate from the other reagents to ensure stability of the enzyme. Upon mixing with the remaining reagents in the reaction mix, the buffering agent becomes sufficiently diluted so as not to significantly mask a pH change. In addition, primers for specific genes of interest may be provided in a separate solution or in a lyophilized form.

[0051] In some embodiments, the amplification reaction is performed within a microtube. In other embodiments, the amplification reaction is performed within a fluidic or microfluidic structure. In some embodiments, the fluidic or microfluidic structure is a well, chamber, or channel that receives the reagents and the nucleic acid sample separately, and then mixes the components together. In another embodiment, the fluidic or microfluidic structure is a well, chamber, or channel that receives the pre -mixed reaction mix. In a further embodiment, the fluidic or microfluidic structure possesses a long optical path for colorimetric observation, or a fluorescent/ absorbance excitation source and detector. In another embodiment, the fluidic or microfluidic structure receives the reagents in a lyophilized form, and subsequently receives the nucleic acid sample and hydration solution. In an embodiment, a chamber fluidic or microfluidic structure has a channel depth ranging between 50 μιη-400 μιη or greater. In a further embodiment, colorimetric observation is accomplished for channel depths (path length) of 50 μιη, 50 μιη-400 μιη, or 50 μιη or greater.

[0052] Some embodiments include a kit for colorimetric detection of an amplification product. The kit may include one or more halochromic agents, one or more enzymes for catalyzing an amplification reaction, and instructions for contacting a sample with a reaction mix including the buffer and the enzyme and the halochromic agent under conditions that an amplification reaction occurs and produces an amplification reaction product if the sample contains a target nucleic acid template molecule, the reaction mix having a starting pH, and if the target nucleic acid template molecule is present, the amplification reaction changes the starting pH of the reaction mix to cause a detectable colorimetric change of the halochromic agent, thereby indicating the presence of the target nucleic acid, and if the target nucleic acid template molecule is not present, the amplification reaction does not generate a sufficient number of protons to change the starting pH of the reaction mix sufficient to cause a detectable colorimetric change of the halochromic agent, thereby indicating that the amplification reaction product has not been produced. In another embodiment, the instructions are for contacting a nucleic acid template molecule with the halochromic agent and enzyme in a reaction mix, under conditions that result in (1) an amplification reaction that amplifies the nucleic acid template molecule to produce an amplification reaction product, and (2) generation of a sufficient number of protons so that an ending pH of the reaction mix is sufficiently low to produce a detectable colorimetric change of the halochromic agent, thereby indicating that the amplification reaction product has been produced. In further embodiments, the kit also includes an acid or base, dNTPs, primers, and monovalent cations. In a further embodiment, the kit includes the following reagents at the following concentrations:

• Bst or Bst 2.0 polymerase, at least 0.8 Unit per microliter;

• Betaine at 0.8 M;

• Primers at 3.6 μΜ total;

o FIP and BIP primers at 1.6 μΜ

o F3 and B3 at 0.2 μΜ

• Magnesium sulfate at 8 mM;

• Ammonium sulfate at 10 mM;

• Potassium chloride at lOmM;

• Sodium hydroxide to set the starting pH of the reaction mix;

• Tween20 at 0.1%;

• dNTP's at 1.4 mM each;

• Phenol red at 50 μΜ.

In a further embodiment, the kit includes LoopF and LoopB primers at 0.8 μΜ each. Methods of the invention

[0053] The amplification reaction amplifies nucleotides from a nucleic acid template. In some embodiments, the amplification reaction is an isothermal amplification reaction, such as a strand displacement reaction. In a further embodiment, a strand displacement reaction is provided by a polymerase with strand displacement activity under reaction conditions such that strand displacement is possible. Examples of strand displacement reactions include strand displacement amplification (SDA), multiple displacement amplification (MDA), rolling circle amplification (RCA) or loop mediated isothermal amplification (LAMP). In other embodiments, the amplification reaction includes other non-isothermal amplification reactions such as polymerase chain reaction (PCR).

[0054] In certain embodiments, the amplification reaction performed is LAMP. In a LAMP reaction, a double- or single-stranded DNA template in dynamic equilibrium at an elevated temperature is amplified using two or three pairs of primers. The primers are designed based on the DNA template, using primer design software such as LAMP Designer (Premier Biosoft, Palo Alto, CA). In the first step of the LAMP reaction, the F2 region of the FIP (Forward Inner Primer) anneals to the single stranded DNA at the respective complementary (F2c) position. Next, a polymerase with strand displacement activity incorporates dNTPs along the template from the 3' end of F2. The incorporation of nucleotides releases protons, reducing the pH of the reaction mix. Then, the F3 forward primer anneals to the F3c region upstream of the F2 region and on the template. The F3 forward primer begins amplifying the template strand, which releases further protons and displaces the FlP-incorporated strand that was synthesized previously. This single strand contains an Fl sequence (within the target sequence) along with its complementary Flc sequence (within the FIP). This forms a stem- loop as Flc anneals to Fl at the 5' end. At the same time, the BIP (Backward Inner Primer) anneals to the other end of the strand and nucleotides extend from B2, releasing more protons. The backward primer B3 then binds to the B3c region, downstream of the B2 region, displaces the BlP-amplified strands and promotes extension to create the double strand. This displaced strand now contains a Bl sequence (within the target sequence) along with its complementary Blc sequence (within the BIP), forming another stem loop in the 3' end. The structure now has two stem-loop structures at each end from which continuous displacement and extension occur to amplify the template. The LAMP reaction can be amplified by adding further Forward and Backward Loop primers to produce more amplicons with stem loop structures. [0055] The LAMP procedure can take place at a fixed temperature, minimizing the need for any expensive thermocycling equipments. Typically, isothermal methods require a set temperature, which is determined by the selected reagents. For example, enzymes function best between 60-65°C in LAMP methods.

[0056] Colorimetric detection of the nucleic acid amplification reaction product can be performed in real-time throughout the amplification reaction, or after the performance of the amplification reaction. Detection of the colorimetric change of the reaction mix can be associated with a digital indication of a presence or absence of the amplification reaction product. In other words, a visual observation of the color change of the reaction mix can provide information regarding whether the amplification reaction product is present or absent. In certain embodiments, detection of a colorimetric change of the reaction mix indicates that the exponential or plateau phase of the amplification reaction has been obtained.

[0057] In some embodiments, detection of the amplification reaction product is accelerated relative to an amplification reaction that uses a reaction mix without a halochromic agent. In further embodiments, the colorimetric change of the reaction mix is detected in less than 60 minutes from a starting time of the amplification reaction. Accelerated detection of the amplification reaction product is obtained because the halochromic agent (a weak acid or base) in the reaction mix absorbs protons generated during the amplification reaction, and recombination of the free protons acts to accelerate the detection of the amplification reaction. The reaction can be designed so that minimal amplification is required to generate a pH transition sufficient for the halochromic agent to change color. Conventional

amplification techniques that use fluorescent intercalating dyes, molecular beacons, hybridization probes, dye-based detection, UV-Vis, or other detection methods require a certain threshold amount of amplification to occur before an amplification signal is detectable. However, the methods of the present invention require a relatively smaller threshold amount of amplification before a color change of the halochromic agent is detectable, and therefore the detection of an amplification reaction product is accelerated relative to conventional amplification methods.

[0058] In some embodiments, the amplification reaction product is detected visually by observation of a color change of the reaction mix. In a further embodiment, the human eye is used for the visual detection. In another embodiment, a camera, a computer, or some other optical device is used for the visual detection or for imaging the reaction mix. Imaging programs include Photoshop (Adobe, San Jose CA), ImageJ (National Institutes of Health, Bethesda MD), and MATLAB (MathWorks, Natick MA). In another embodiment, the amplification reaction product is detected by measuring fluorescence of the reaction mix, using fluorescence spectroscopy methods. In another embodiment, the amplification reaction product is detected by measuring absorbance of the reaction mix, using absorption

spectroscopy methods. In a further embodiment, the endpoint or overall change in absorbance or fluorescence of the reaction mix is measured at a given wavelength or set of wavelengths.

EXAMPLES

[0059] Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for.

[0060] The practice of the present invention will employ, unless otherwise indicated, conventional methods of protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., T.E. Creighton, Proteins: Structures and Molecular Properties (W.H. Freeman and Company, 1993); A.L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al, Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.);

Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pennsylvania: Mack Publishing Company, 1990); Carey and Sundberg Advanced Organic Chemistry 3 ^rd Ed. (Plenum Press) Vols A and B(l 992).

Example 1: Colorimetric Detection of a Nucleic Acid Amplification Reaction Product

[0061] In an assay for colorimetric detection of a nucleic acid amplification reaction product, the following reagents were mixed together to produce a 2X reagent mix:

• Magnesium Sulphate (Sigma Aldrich) at 16 mM

• Ammonium Sulphate (Sigma Aldrich) at 20 mM

• Potassium Chloride (Sigma Aldrich) at 20mM

• Sodium hydroxide (Sigma Aldrich) at a concentration that sets the starting pH of the reagent mix to 8.8 pH [0062] The reagent mix was adjusted to an initial pH of 8.8 to enable efficient initial polymerization. The reagent mix was autoclaved for 1 hour for sterilization. The following ingredients were then added (in a sterile form) to the reagent mix to generate the reaction mix:

• Tween20 (Sigma Aldrich) at 0.1 % (v/v)

• dNTPs (NEB) at 1.4 mM each

• Phenol Red (Sigma Aldrich) at 50 μΜ

• Bst polymerase (NEB) at 0.8 Unit per microliter (the enzyme storage buffer contributing 1 mM Tris buffer, 5 mM KC1, 0.01 mM EDTA, 0.1 mM DTT, 0.01 % Triton X-100 (v/v) and 5% Glycerol ((w/v) to the reaction mix)

• Betaine (Sigma Aldrich) at 0.8 M

[0063] Primers and a nucleic acid template were added to the reaction mix. The primers were designed for LAMP and included two pairs of primers (solubilized in IX Tris EDTA buffer) at a total concentration of 3.6 μΜ as described above. Primer F3 has the sequence:

GATCTGAATCCGACCAACCG (SEQ ID NO: 1); primer B3 has the sequence:

AACGCCCACGCTCTCGCA (SEQ ID NO: 2); the primer FIP has the sequence:

AAATCCGTCCAGTGGTTTTTTTGAAAATCGTTGTATCTCCG (SEQ ID NO: 3); and the primer BIP has the sequence:

CCGAAACCACTGGACGGATTTTTATTTTTAATCTAAAACAAACATC (SEQ ID NO: 4). The nucleic acid template molecule was purified from Schistosoma mansoni. FIG. 1 shows the SMI -7 target region of the nucleic acid template molecule (see Hamburger et al, Detection of Schistosoma mansoni and Schistosoma haematobium DNA by Loop-Mediated Isothermal Amplification: Identification of infected Snails from Early Prepatency, Am J Trop Med Hyg, 2010). The positive test reactions contained template DNA, and the negative control reactions contained water. The reaction mixes had a starting pH in the range of 7.5 - 8.5. The reaction mixes were heated in micro-tubes to 63°C on a thermocycler to allow template amplification. After a predetermined reaction period of 45 minutes, during which sufficient template amplification occurred, the resultant color of the reaction mix was visually observed.

[0064] During the amplification process, the pH of the reaction mix was reduced from 7.5- 8.5 to around 6.6 in a repeatable fashion. FIG. 2 is a graph showing the pH measurements for repeated positive (test) and negative (negative control) amplification reactions. The halochromic agent used was Phenol red, which has a transition pH range of 6.8 - 8.2. Phenol red changes color over this transition pH range from red to yellow (when the pH is lowered from the upper pH limit to the lower pH limit). In the assay, the reaction mix changed color from red (at pH 8.0) to yellow (at pH 6.6) in response to the pH change during nucleic acid amplification. FIG. 3 is a graph showing the difference in contrast value using HSV (hue, saturation, value) of images of the reaction mixes of a positive and negative amplification reaction at the reaction endpoints. The color change is quantitatively demonstrated in the hue variable. To confirm that the color change was due to target DNA amplification, endpoint reactions were analyzed using gel electrophoresis to verify the presence of amplicons (FIG. 4)·

[0065] Using this method, amplification of a DNA template can be easily observed, either at the reaction end-point or in real-time throughout the reaction, by visually observing the color change in the reaction mix, or by measuring the absorbance or fluorescence of the reaction mix. This mechanism generates much larger contrast in comparison to other colorimetric detection techniques and can be imaged without the need of expensive optical

instrumentation.

Example 2: Detection of LAMP Amplification Using a Visual Halochromic Agent

[0066] LAMP reactions were performed with a reaction mix comprising of: 10 mM

(NH4) ₂ S04, 15 mM KC1, 0.1 mM EDTA, 0.1 mM DTT, 0.01 % Triton X-100 (v/v), 5 % Glycerol, 8 mM MgS0 ₄ , 1.4 mM each dNTPs, 0.1% v/v Tween-20, 0.8 M Betaine. Three primer pairs, specific to different targets, were added to a final concentration of 1.6 μΜ each for FIP/BIP, 0.2 μΜ each for F3 /B3, 0.4 μΜ each for LoopB/F. The final reaction volume is 10 μΐ _^ and was held at 63 °C for different incubation times.

[0067] In FIG. 5, the final Tris buffer concentration of the reaction mix was varied from 0.34 mM to 19 mM (by varying amount of Tris buffer formulated to pH 8.8). Reactions were performed with primers for lambda phage DNA, 5 ng of lambda DNA (New England Biolabs), 0.8 U/μΙ Bst 2.0 DNA polymerase (New England Biolabs) and 0.2 mM Neutral Red (Sigma Aldrich). The reaction tubes were then imaged and the Normalized Hue value was calculated for the color of the reaction mix. The Normalized Hue value was defined as the difference in Hue values between a positive and a no-template negative reaction. A color change, indicated by a change in the Normalized Hue value above the visualization threshold (dotted line), was observed for buffer concentrations as high as 19mM Tris. This indicates that reaction mix with buffer capacities equivalent to >lmM and <19mM Tris allow enough pH change for visual color change detection.

[0068] In FIG. 6, the tolerance of this visual detection method to excess hydronium ions added to the reaction mix was evaluated. This tolerance is important to allow the use of a wide variety of DNA samples which can add a range of hydronium or hydroxide ion equivalents to the reaction. Reactions were performed with 2mM final Tris buffer concentration, 5 ng lambda DNA target, 0.8 υ/μί Bst DNA polymerase and 0.2 mM Neutral Red halochromic agent. The change in Normalized Hue value indicates that this visual detection chemistry works with 4.8 x 10 ^"9 till 4.8xl0 ^"18 additional hydronium ion equivalent per 10 uL reaction.

[0069] In FIGs. 7A-7D, the compatibility of different pH indicators and amplification targets with visual detection of LAMP amplification was evaluated. The reactions were performed with final Tris buffer concentration in the range of 1.2 - 1.3 mM and 0.8 Bst DNA polymerase. Three different indicator were tested with 5 ng lambda DNA target: 50 μΜ Phenol Red, 260 μΜ Cresol Red and 160 μΜ Bromothymol Blue (FIG. 7A). High contrast change in the normalized hue value was observed for all indicators tested.

[0070] Concentration sweeps were also performed for these indicators Bromothymol Blue (FIG. 7B top left), Cresol Red (FIG. 7B top right), Neutral Red (FIG. 7B bottom left) and Phenol Red (FIG. 7B bottom right) with Lambda target, which demonstrated the wide range of concentrations that are compatible with the chemistry. LAMP assays using 130 ng Schistosoma mansoni gDNA with 50 μΜ Phenol Red (FIG. 7C) and Human GAPDH mRNA with 0.2 mM Neutral Red (FIG. 7D) were also tested visual detection of these targets was demonstrated at end-point.

[0071] In FIG. 8, the compatibility of different polymerases with visual detection of LAMP amplification was evaluated. The reactions were performed with 1.3 mM final Tris buffer concentration, 5 ng lambda DNA target and 0.2 mM Neutral Red. 0.8 U/μΙ of two different polymerases, Bst 2.0 and Gspm 2.0 (OptiGene), were used. High contrast color change was observed for both polymerases after 60 minutes of incubation (FIG. 8).

Table 2: Sequences Used

Lambda Loop F SEQ ID NO: 9

Lambda Loop B SEQ ID NO: 10

Schistosoma F3 SEQ ID NO: 1

Schistosoma B3 SEQ ID NO: 2

Schistosoma FIP SEQ ID NO: 3

Schistosoma BIP SEQ ID NO: 4

GAPDH F3 SEQ ID NO: 11

GAPDH B3 SEQ ID NO: 12

GAPDH FIP SEQ ID NO: 13

GAPDH BIP SEQ ID NO: 14

GAPDH Loop F SEQ ID NO: 15

GAPDH Loop B SEQ ID NO: 16

Example 3: Visual Detection of LAMP Amplification in Sub-Millimeter Path Lengths

[0072] LAMP reactions were performed as in Example 1 with 1.3 mM final Tris buffer concentration (buffer formulated to pH 8.8), 0.8 U/μΙ of Bst 2.0 DNA Polymerase, 5 ng lambda DNA template and 0.2 mM Neutral Red or 160 μΜ Bromothymol Blue. Both the positive and the no-template negative reactions were added after amplification to flow chambers with varying channel depths (FIG. 9A for Neutral Red and FIG. 9B for

Bromothymol Blue). These flow chambers were machined in acrylic with channel depths ranging from 50 μιη to 400 μιη. High contrast color difference (above the visual detection threshold; dotted line) between the positive and the negative reactions was observed for channel depths of 50 μιη and above. This demonstrates that this visual detection chemistry is amenable for use in reaction chambers with sub-milimeter path lengths (depths) and above. Such reaction chambers can be used to reduce the amount of reagents used and to allow multiple reactions to take place in a certain footprint (eg. in a microfluidic cartridge).

Example 4: Detection of Strand Displacement Amplification (SDA) Using a Visual Halochromic Agent

[0073] SDA reactions were performed using a reaction mix comprising of: 1.3 mM final Tris buffer concentration (buffer formulated to pH 8.8), 10 mM (NH4) ₂ S04, 50 mM KC1

(adjusted to pH 8.5), 8 mM MgS0 ₄ , 4.4 mM each dATP, dGTP, dTTP, 0.8 mM dCTP-aS

(TriLink Biotechnologies), 0.1% v/v Tween-20, 0.8 M Betaine, 0.32 U/μΙ Bst DNA polymerase (New England Biolabs), 0.2U/uL BSoBI (New England Biolabs) and 0.2 mM Neutral Red halochromic agent. Primers designed for human BRCA1 (SDAf: SEQ ID NO: 17; SDAr: SEQ ID NO: 18; BF: SEQ ID NO: 19; BR: SEQ ID NO: 20) were added to the reaction at 0.5 μΜ final concentration each. 5 ng of HeLa gDNA was added to a final reaction volume of 25 and was held at 65 °C for different incubation times. A change in Normalized Hue value over time (FIG. 10) indicates that this visual detection chemistry works with SDA.

Example 5: Detection of PCR Amplification Using a Visual Halochromic Agent

[0074] PCR reactions were performed using a reaction mix comprising of: 50 mM KCl and 2 mM MgCl ₂ (pH adjusted 8.5), 0.5 mM each dNTP, 5U Taq DNA polymerase (New England Biolabs) and 0.2 mM Neutral Red halochromic agent. Total carry-over Tris-HCl

concentration from enzyme storage buffer and primers (Forward: SEQ ID NO: 21; Reverse: SEQ ID NO: 22) was 1.15 mM in the final reaction mix. Primers were designed for

Escherichia coli 16s rRNA gene and added to the reaction at 0.5 μΜ final concentration each. 10 ng of E.coli gDNA was added to a final reaction volume of 25 and was initially held at 95 °C hold for 2 min, followed by 50 cycles of 95 °C for 10 sec, 55 °C for 30 sec, 68 °C for 30 sec. A change in Normalized Hue value over time (FIG. 11) indicates that this visual detection chemistry works with PCR.

Example 6: Increase in Visual Detection Contrast with Combination of

Halochromic Agents

[0075] LAMP reactions were performed as in Example 1 with 1.3 mM final Tris buffer concentration (buffer formulated to pH 8.8), 0.8 U/μΙ of Bst 2.0 DNA Polymerase and 5 ng lambda DNA template. The color change contrast was evaluated for Phenol Red at 50 μΜ concentration and combination of Phenol Red and Bromothymol Blue at 50 μΜ and 160 μΜ concentrations respectively (FIG. 12A). The color change contrast was also evaluated for Cresol Red at 260 μΜ concentration and combination of Cresol Red and Bromothymol Blue at 260 μΜ and 160 μΜ concentrations respectively (FIG. 12B). The contrast values were calculated from the RGB values of images of the reaction mix using the formula: 0.299R + 0.587G + 0.114B. The normalized contrast change was defined as the difference between positive and negative reaction contrast values normalized to the background. The increase in the normalized contrast change with the use of the halochromic agent combination demonstrates the utility of such combinations. Example 7: Real-time Color Monitoring of Amplification for Quantification Using Visual Halochromic Agents

[0076] LAMP reactions were performed as in Example 1 with 1.3 mM final Tris buffer concentration (buffer formulated to pH 8.8), 0.8 U/μΙ of Bst 2.0 DNA Polymerase, Phenol

Red and Bromothymol Blue at 50 μΜ and 160 μΜ concentrations respectively and varying lambda DNA template concentrations. Color change contrast was evaluated for lambda DNA target at 0.5 fg/μΐ, 0.05 pg/μΐ and 0.5 pg/μΐ final concentrations. The contrast values were calculated from the RGB values of images of the reaction mix as described in Example 5.

The results (FIG. 13) indicate that the higher DNA concentrations led to a detectable change in visual contrast earlier than the lower DNA concentrations. Hence, we demonstrate the ability to distinguish between different target concentrations with the real-time color monitoring of this chemistry.

[0077] While the invention has been particularly shown and described with reference to a preferred embodiment and various alternate embodiments, it will be understood by persons skilled in the relevant art that various changes in form and details can be made therein without departing from the spirit and scope of the invention.

[0078] All references, issued patents and patent applications cited within the body of the instant specification are hereby incorporated by reference in their entirety, for all purposes.