TWO DIMENSIONAL LAYER MATERIALS

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent Application Serial Number

62/448,078, filed on January 19, 2017, which is incorporated herein by reference in its entirety.

FIELD

The present disclosure relates to nanofabrication of biomolecular sensing devices.

More particularly, the present disclosure relates to the fabrication of devices for analyzing DNA and related biomolecules, wherein the devices contain two dimensional layer materials.

BACKGROUND

Analysis of biomolecules including DNAs and genomes has received an increasing amount of attention in recent years in various fields of precision medicine or nanotechnology. The seminal work of Maclyn McCarty and Oswald T. Avery in 1946 (see, "Studies On The Chemical Nature Of The Substance Inducing Transformation Of Pneumococcal Types II. Effect Of Deoxyribonuclease On The Biological Activity Of The Transforming Substance," The Journal of Experimental Medicine 83(2), 89-96 (1946)), demonstrated that DNA was the material that determined traits of an organism. The molecular structure of DNA was then first described by James D. Watson and Francis HC Crick in 1953, (see a published article, "Molecular structure of nucleic acids.", Nature 171,737-738 (1953)), for which they received the 1962 Nobel Prize in Medicine. This work made it clear that the sequence of chemical letters (bases) of the DNA molecules encode the fundamental biological information. Since this discovery, there has been a concerted effort to develop means to actually experimentally measure this sequence. The first method for systematically sequencing DNA was introduced by Sanger, et al in 1978, for which he received the 1980 Nobel Prize in Chemistry. See an article, Sanger, Frederick, et al., "The nucleotide sequence of bacteriophage φΧ174." J. Mol. Bio. 125, 225-246 (1978).

Sequencing techniques for genome analysis evolved into utilizing automated commercial instrument platform in the late 1980's, which ultimately enabled the sequencing of the first human genome in 2001. This was the result of a massive public and private effort taking over a decade, at a cost of billions of dollars, and relying on the output of thousands of dedicated DNA sequencing instruments. The success of this effort motivated the development of a number of "massively parallel" sequencing platforms with the goal of dramatically reducing the cost and time required to sequence a human genome. Such massively parallel sequencing platforms generally rely on processing millions to billions of sequencing reactions at the same time in highly miniaturized microfluidic formats. The first of these was invented and commercialized by Jonathan M. Rothberg's group in 2005 as the 454 platform, which achieved thousand fold reductions in cost and instrument time. See, an article by Marcel Margulies, et al., "Genome Sequencing in Open Microfabricated High Density Picoliter Reactors," Nature 437, 376-380 (2005). However, the 454 platform still required approximately a million dollars and took over a month to sequence a genome.

The 454 platform was followed by a variety of other related techniques and commercial platforms. See, articles by M. L. Metzker, " Sequencing Technologies— the Next Generation," Nature Rev. Gen. 1 1 (1), 31 -46 (2010), and by C. W. Fuller et. al, "The Challenges of Sequencing by Synthesis," Nature Biotech. 27(1 1), 1013-1023 (2009). This progress lead to the realization of the long-sought "$1 ,000 genome" in 2014, in which the cost of sequencing a human genome at a service lab was reduced to approximately $1 ,000, and could be performed in several days. However, the highly sophisticated instrument for this sequencing cost nearly one million dollars, and the data was in the form of billions of short reads of approximately 100 bases in length. The billions of short reads often further contained errors so the data required interpretation relative to a standard reference genome with each base being sequenced multiple times to assess a new individual genome.

Thus, further improvements in quality and accuracy of sequencing, as well as reductions in cost and time are still needed. This is especially true to make genome sequencing practical for widespread use in precision medicine (see the aforementioned article by Fuller et al), where it is desirable to sequence the genomes of millions of individuals with a clinical grade of quality.

While many DNA sequencing techniques utilize optical means with fluorescence reporters, such methods can be cumbersome, slow in detection speed, and difficult to mass produce to further reduce costs. Label-free DNA or genome sequencing approaches provide advantages of not having to use fluorescent type labeling processes and associated optical systems, especially when combined with electronic signal detection that can be achieved rapidly and in an inexpensive way. While current molecular electronic devices can electronically measure molecules for various applications, they lack the reproducibility as well as scalability and manufacturability needed for rapidly sensing many analytes at a scale of up to millions in a practical manner. Such highly scalable methods are particularly important for DNA sequencing applications, which often need to analyze millions to billions of independent DNA molecules. In addition, the manufacture of current molecular electronic devices is generally costly due to the high level of precision needed.

SUMMARY

In various embodiments described herein, specially processed, 2D layer-containing enzyme polymerase sensor device structures and methods of manufacture for a multitude of devices for use in electronic DNA, RNA or genome sequencing systems are disclosed. Such label-free, single molecule based sequencing analysis systems utilize preferably a microstructurally controlled transition metal dichalcogenide (TMD) layer with intentionally defective structures, so as to utilize altered bandgaps and enhanced attachment of single biomolecules such as enzyme polymerase molecules. The electronic system may also be used in analyzing other types of biomolecules, such as proteins, depending on how the molecular sensors are functionalized to interact with biomolecule sensing targets. The TMD-based sequencing systems invented here can be assembled into a massively parallel configuration for rapid analysis of targets including nucleotides, in particular for applications to sequencing of a DNA molecule, or a collection of such molecules constituting an entire human genome.

In an aspect, a sequencing device is disclosed. The sequencing device includes an electrode array of conducting electrode pairs, each pair of electrodes comprising a source and a drain electrode separated by a nanogap, said electrode array deposited and patterned on a dielectric substrate; a single-layer or few-layer thick transition metal dichalcogenide (TMD) layer disposed on each pair of electrodes, connecting each source and drain electrode within each pair, and bridging each nanogap of each pair; a dielectric masking layer disposed on the TMD layer and comprising size-limited openings that define exposed TMD regions, each opening sized so as to allow only a single enzyme biomolecule to fit therein and to attach onto the exposed TMD region defined by each opening; an enzyme molecule attached to each exposed TMD region such that only one enzyme molecule is found within each opening; and a microfluidic system encasing the electrode array, wherein attachment or detachment of a biomolecule selected from the group consisting of a nucleotide monomer, a protein, and a DNA segment, onto the enzyme molecule, one at a time, can be monitored as a uniquely identifiable electrical signal pulse to determine the specific nature of the biomolecule attaching or detaching. In embodiments, the TMD is selected from M0S2, WS2, TiS ₂ , ZrS2, HfS ₂ , VS ₂ , NbS ₂ , TaS ₂ , TcS ₂ , ReS ₂ , CoS ₂ , RhS ₂ , IrS ₂ , NiS ₂ , PdS ₂ , PtS ₂ and their modifications or combinations, including modified stoichiometry of sulfur contents having MX _(2-X) or MX _(2+X) wherein x is in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. In embodiments, the sulfur stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects so as to increase the surface energy and enhance the adhesion of biomolecule to the bridge sensor, increasing the bandgap for stronger electrical signal pulse. In embodiments, the TMD is selected from MoSe ₂ , WSe ₂ , or TiSe ₂ , ZrSe ₂ , HfSe ₂ , VSe ₂ , NbSe ₂ , TaSe ₂ , TcSe ₂ , ReSe ₂ , CoSe ₂ , RhSe ₂ , IrSe ₂ , NiSe ₂ , PdSe ₂ , PtSe ₂ and their modifications or combinations, including modified stoichiometry of selenium contents having MX _(2-X) or MX _(2+X) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. In embodiments, the selenium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects in order to increase the surface energy of the TMD layer and enhance the adhesion of biomolecule to the bridge sensor for stronger sensor signals. In embodiments, the TMD is selected from MoTe ₂ , WTe ₂ , or TiTe ₂ , ZrTe ₂ , HfTe ₂ , VTe ₂ , NbTe ₂ , TaTe ₂ , TcTe ₂ , ReTe ₂ , CoTe ₂ , RhTe ₂ , IrTe ₂ , NiTe ₂ , PdTe ₂ , PtTe ₂ and their modifications or combinations, including modified stoichiometry of tellurium contents having MX( _2-X ) or MX( _2+X ) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. In embodiments, the tellurium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects in order to increase the surface energy of the TMD layer and enhance the adhesion of biomolecule to the bridge sensor for stronger sensor signals. In embodiments, the TMD comprises a mixed TMD selected from TMD compounds in which the MX ₂ compound has mixed metals and/or mixed chalcogenide, selected from the group consisting of Mo(S _x Se _y Te _z ) ₂ , W(S _x Se _y Te _z ) ₂ , Ti(S _x Se _y Te _z ) ₂ , Zr(S _x Se _y Te _z ) ₂ , Hf(S _x Se _y Te _z ) ₂ , V(S _x Se _y Te _z ) ₂ , Nb(S _x Se _y Te _z ) ₂ , Ta(S _x Se _y Te _z ) ₂ , Tc(S _x Se _y Te _z ) ₂ , Re(S _x Se _y Te _z ) ₂ , Co(S _x Se _y Te _z ) ₂ , Rh(S _x Se _y Te _z ) ₂ , Ir(S _x Se _y Te _z ) ₂ , Ni(S _x Se _y Te _z ) ₂ , Pd(S _x Se _y Te _z ) ₂ , and Pt(S _x Se _y Te _z ) ₂ wherein the combined (x + y + z) is 1 - 3, 0.5 - 1.5, or 0.7 - 1.3. In further embodiments, two or more metals are combined for sulfur containing, Se-containing or Te-containing TMD layers. In embodiments, the TMD layer comprises Mo _x W _y Co _z )S ₂ or (Hf _x W _y Co _z )Te ₂ . In embodiments, the TMD comprises a M ₍ i _-W) N _y X(2- _Z) Y _z structure in which the transition metal M is partially substituted with non- transition elements N, with a concentration of w and the N element selected from one or more of Al, Si, Ga, Ge, In, Sn, Sb, Bi, Al, Na, K, Ca, Mg, Sr, Ba, with the w value in the range of 0 - 0.3, and the chalcogenide element X partially substituted with a non-chalcogenide element Y, with the Y element selected from one or more of Li, B, C, N, O, P, F, CI, I, with the z value in the range of 0 - 0.3. In embodiments, the metallic conducting electrode pair is selected from Au, Pt, Ag, Pd, Rh, or their alloys. In embodiments, the nanogap is about 2 nm to about 20 nm. In embodiments, the size-limited openings are preferably less than 30 nm average equivalent diameter each, more preferably less than about 20 nm equivalent diameter, even more preferably less than about 10 nm equivalent diameter, by lithographically defined coverage of dielectric material layer of polymer or ceramic outside a specific region intended for attaching only a single molecule. In embodiments, the size- limited openings are about 30 nm equivalent diameter each, or about 20 nm equivalent diameter each, or about 10 nm equivalent diameter each, and wherein the TMD layer comprises an intentionally damaged structure with insulator or very high resistivity characteristics serving as the mask material to enable single molecule attachment; with at least 100 ohm-cm, preferably at least 10,000 ohm-cm, even more preferably at least 1 mega ohm-cm resistivity for the regions outside a specific region intended for attaching only a single molecule; and with the intentional damaging performed by electron bombardment, laser radiation bombardment, ion bombardment, or ion implant doping.

In further embodiments, the TMD layer is defective with the defects selected from linear nano-ribbon parallel array, patterned shape nano-ribbon array, strained lattice defects, vacancies, interstitial defects, dislocation defects, foreign atom implanted defects, or nanoporous defects. In embodiments, the size-limited TMD layer contains strained lattice defects, vacancies, interstitial defects, dislocation defects or foreign atom implanted defects with a defect density of at least about 10 ⁵ /cm ² . In embodiments, the defects in the TMD layer are nanoporous defects having an equivalent diameter of at least 2 nm with a defect density of at least about lo cm ² . In embodiments, the TMD layer is defective with the bandgap opened additionally by at least 0.2 eV, preferably by at least 0.5 eV compared to the TMD without defects. In embodiments, the TMD layer surface exhibits hydrophilic characteristics with a hydrophilic area having a water droplet contact angle of at most 50 degrees, preferably at most 30 degrees, even more preferably at most 15 degrees; with an improved biomolecule attachment frequency with the adhesion improvement by at least 30%, preferably by at least 50%, even more preferably by at least 100% increased adhesion event as compared to the all hydrophobic TMD surface during microfluidic chamber processing of fluid supplying to provide biomolecules, nucleotides, and related biological or chemical components, as well as washing or fluid replacement operations; and the hydrophilic characteristics are associated with defects including strained lattice, vacancies, interstitials, dislocations, nanopores, nano- pinholes, foreign atom doping, with the defect density being at least about lo cm ² , and preferably at least about 10 ⁵ /cm ² . In embodiments, the TMD layer surface consists of a mixed structure of a hydrophilic region and a hydrophobic region, and the hydrophilic area has a water droplet contact angle of at most 50 degrees, preferably at most 30 degrees, even more preferably at most 15 degrees; the area fraction of the hydrophilic region is at least 10%, preferably at least 30%, even more preferably at least 50% area fraction of the exposed TMD surface to attract a single biomolecule; the hydrophilic regions are in the form of circular, oval, rectangular, or irregular islands, or in a striped configuration; the TMD surface has defects such as vacancies, interstitials, dislocations or aggregated defects, nanopores, chemically doped regions with foreign atoms, or striped pores, with the density of such defects being at least lo cm ² , preferably at least 10 ⁵ /cm ² , and such a composite hydrophilic- hydrophobic configuration enables improved biomolecule attachment frequency with the adhesion improvement by at least 30%, preferably by at least 50%, even more preferably by at least 100% increased adhesion event as compared to the all hydrophobic TMD surface during microfluidic chamber processing of fluid supplying to provide biomolecules, nucleotides, and related biological or chemical components, as well as washing or fluid replacement operations; and/or the size of either hydrophilic islands or hydrophobic islands is desirably 1-30 nm, preferably 1-10 nm, and more preferably 1-5 nm. In further embodiments, the TMD layer has tunable hydrophilicity, wherein: the TMD layer is either suspended between two electrodes or fixed on top of two electrodes without suspended structural configuration; the TMD bridge surface is size-limited for attachment of single biomolecule; on-demand switching of hydrophobic to hydrophilic surface state is enabled by a device configuration of at least a pair of vertical electrodes positioned below and above the sensor bridge structure so as to apply electric field of at least 10 V/nm, preferably at least 30 V/nm to alter the semiconducting properties and widen the bandgap by at least 5%, preferably at least 10%, and make the TMD more hydrophilic with the water droplet contact angle to decrease by at least 5 degrees, preferably by at least 20 degrees for easier accommodation of microfluidic chamber environment and improved adhesion probability of single enzyme molecule such as DNA or RNA polymerase increasing by at least 30%; the electric field applied is a DC electric field or AC electric field; hydrophilic improvement is capable of being reversed to return to hydrophobic state to enable a release of previously used biomolecule and to avoid unnecessary attachment of biomolecules; and/or optionally having at least 1 ,000, preferably as many as 10,000 or even more preferably at least 1 million devices, with one or more selected electrode-paired devices simultaneously or in a series operation tunable to be hydrophilic or hydrophobic. In embodiments, the biomolecule to be attached onto the TMD is a polymerase enzyme. In embodiments, the biomolecule to be attached onto the TMD is selected from various other biopolymers of DNA, RNA, proteins, ribozyme, aptamer or polysaccharide. In embodiments, the two-dimension shaped TMD layer is locally converted to three-dimensionally shaped TMD, so as to provide mechanical support for robust and reliable TMD positioning, with additional defects at the curved or kinked position with displaced or strained lattice in TMD, to produce higher-energy-state positions for enhanced adhesion of enzyme biomolecules, with the altered shape TMD having the following structural characteristics of: an introduction of new modes of defects and shape discontinuity for higher-energy-state local regions; a shape-altering insert structure made of dielectric material selected from polymer materials or ceramics materials; the shape-altering insert structure having a uniformly or non-uniformly protruding structure beyond the level of metallic conductor electrode top surface so as to make the TMD layer non-flat geometry selected the configuration of being bent, curvatured, dome-shaped, irregular-shaped, buckled, or locally punctured shape and introduce displaced; the shape-altered TMD layer already possessing a defective structure comprising lattice defects of strained lattice, vacancies, interstitials, dislocations, nanopores, chemically doped regions with a defect density of at least 10 /cm ² ; the altered shape selected from hemispherical, rectangle, oval, wavy, or other periodic or irregular geometry; and/or the shape-altering insert permanently left underneath the TMD layer to serve as a beneficial mechanical support to guard against mechanical detachment or damage of the TMD layer during microfluidic handling of the sequencing device systems and associated inadvertent force applied to the suspended or barely bonded TMD layer on the nanogap region, or etched away to leave a mechanically compliant, protruding TMD layer.

In further embodiments, the TMD layer is in contact with the dielectric substrate with no nanogap, and a pair of metallic electrodes extend from both ends of the TMD island as electric lead wires. In further embodiments, the polymerase enzyme connection to the TMD surface is via functional groups or functional group pairs selected from a list of streptavidin- biotin pair, antigen-antibody interaction, bifunctional ligands using mercaptocarbonic acids [HS-(CH ₂ )n-COOH, n = l-15], peptide functional groups, thiol-alkyne pair, COOH-NH ₂ functional group pair, a thiol-maleimide azide pair, silanization linkage using mercaptosilane compounds, and a NHS (N-hydroxysuccinimide) ester-amine pair. In embodiments, the dNTP nucleotide being attached to the enzyme polymerase molecule is a modified nucleotide type to enhance the incorporation signals, or produce signals with enhanced differences between the different base (A, C, G, T) incorporation events, for greater accuracy determining the template sequence, with such dNTP modifications include modifications of: the base, such as 7-deaza forms, 8-bromo forms; the alpha- and beta- phosphates, such as thiolated forms or bromated forms of these phosphates; the gamma-phosphate modifications, including the addition of phosphates, such as tetra-, penta- or hexa- phosphates forms; or the groups added to the terminal phosphate.

In further embodiments, the electrode arrangement comprises a triode configuration with a gate electrode placed parallel to each of said source and drain electrodes or perpendicular to each nanogap between each of source and drain electrodes in the electrode array. In further embodiments, the electrodes, TMD layer, masking dielectric, and enzyme molecule are arranged into an array configuration so as to allow massively parallel electronic sequencing analysis using devices organized into a system having at least 1,000, preferably at least 1 million devices. In embodiments, a sequential interrogation of an array of electrodes in the TMD-containing polymerase enzyme molecular sensor is enabled for DNA or genome sequencing by using a common lead wire on one side of the array. In embodiments, the electrodes, TMD layer, masking dielectric, and enzyme molecule are arranged into a three- dimensional array of molecular electronics genome-sequencing platform using a stacked microfluidic chamber or a common microfluidic chamber for a stacked layer devices, so as to allow massively parallel electronic sequencing analysis using devices organized into a system having at least 1,000, preferably at least 1 million devices.

In another aspect, a method of fabricating a TMD based DNA or genome sequencing device is provided. The method involves providing an array of metallic conducting electrode pairs with a source and drain arrangement deposited and patterned on a dielectric substrate; depositing a single-layer or few-layer TMD by using a liquid container lift-up placement method onto the electrode array, by using a vacuum transfer method, or by using a stamp transfer method; nanopatteming a dielectric masking layer placed on the TMD surface with an opening which is size-limited so as to allow only a single enzyme biomolecule to attach onto the exposed TMD surface for sequencing analysis; placing the sequencing device into a microfluidic system and supplying a fluid containing denaturized nucleotide molecules or modified nucleotides, and chemical agents; and making an electronic measurement and computer analysis on the event of individual nucleotide monomers or modified nucleotide components attachment onto an enzyme polymerase molecule one at a time to obtain electrical pulse signals to determine the specific nature of the nucleotide being attached. In embodiments, the TMD layer is made defective by nanopatterning into linear nano-ribbon parallel array or patterned shape nano-ribbon array, or introducing disturbed lattice defects of strained lattice, vacancies, interstitials, dislocations, chemical doped or ion implant doped regions, or providing nanoporous defects or nano-pinholes defects. In embodiments, the defects in TMD layer are introduced by beam irradiation selected from ion implantation beam, plasma reactive ion etch (RIE) atmosphere, broadened optical, electron, ion or neutron beam, so as to introduce defect density of at least about 10 ⁵ /cm ² . In embodiments, the irradiated structure is post-irradiation annealed at about 100°C to about 600 °C. In embodiments, the TMD lattice defects or nanopores are introduced by chemical etching using oxidizing chemicals, strong acids, strong alkaline solutions, so as to introduce defect density of at least about 10 ⁵ /cm ² . In embodiments, the TMD with nanoporous defects are introduced by using a nano-hole containing template selected from block copolymer or anodized aluminum oxide so as to introduce defect density of at least 10 ⁵ /cm ² . In embodiments, the TMD with nanoporous defects are introduced by using completely deposited thin films comprising nano-pinholes as a mask through which the TMD layer is etched so as to introduce nano-pinholes defect density of at least about 10 ⁵ /cm ² . In embodiments, the TMD with nanoporous defects are introduced by using nanoimprinting patterning so as to introduce defect density of at least 10 ⁵ /cm ² . In embodiments, the TMD with nanoporous defects are introduced by using metallic nanoparticles spray deposited onto TMD, allowing diffusional reactions and differential chemical etching. In embodiments, the TMD layer material outside a specific region that is intended for a single biomolecule to be attached is intentionally damaged, with the crystal structure of TMD material affected and behave like an insulator or very high resistivity material with at least 100 ohm-cm, preferably at least 10,000 ohm-cam, even more preferably at least 1 mega ohm-cm resistivity using a processing methods selected from the group consisting of electron beam irradiation, ion beam irradiation, optical or laser beam irradiation, particle beam irradiation, and ion implantation of foreign species atoms. In embodiments, the TMD layer material is made to exhibit a hydrophilic state obtained by using one or more of the following processing techniques: by using a plasma treatment using oxygen-containing plasma or other types of plasma containing nitrogen, chlorine, fluorine or mixed elements, or by using imperfect crystallization with defects such as strained lattice, vacancies, interstitials, dislocations nanopores or aggregated defects) in the M0S2 structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) at lower temperatures during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process temperature selected to be lower by at least 50 °C, preferably by at least 200 °C lower than the temperature for obtaining high- quality crystallization with more than 90% of the material having well crystallized TMD layer material, or by using a non-completed crystallization process with defects such as strained lattice, vacancies, interstitials, dislocations nanopores or aggregated defects) in the MoS ₂ structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) for shorter time periods during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process time selected to be shorter by a factor of at least 3, preferably by a factor of 10 than the annealing time needed for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material or by a deposition of a thin hydrophilic surface layer less than 10 nm thickness, such as transition metals like Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Fe, Co, Ni, Cu, Zn, or ceramic islands of these elements such as T1O2, NiO, Fe2C>3 using physical deposition, chemical deposition, electrochemical deposition, or ion implantation. In further embodiments, the TMD layer material is made to exhibit a combined hydrophilic and hydrophilic mixed phase state obtained by using one or more of the following processing techniques: by using a plasma treatment using oxygen-containing plasma or other types of plasma containing nitrogen, chlorine, fluorine or mixed elements, or by using imperfect crystallization with at least 10%, preferably at least 30% area fraction of TMD surface material having an imperfect crystal lattice configuration, with defects such as vacancies, interstitials, dislocations nanopores or aggregated defects) in the MoS ₂ structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) at lower temperatures and shorter times during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process temperature selected to be lower by at least 50°C, preferably by at least 200°C lower than the temperature for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material, or by using a non-completed crystallization process with at least 10%, preferably at least 30% area fraction of TMD surface material having an imperfect crystal lattice configuration, with defects such as vacancies, interstitials, dislocations nanopores or aggregated defects) in the M0S2 structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) for shorter time periods during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process time selected to be shorter by a factor of at least 3, preferably by a factor of 10 than the annealing time needed for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material, or by a partial deposition of hydrophilic islands such as metallic islands of transition metals like Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Fe, Co, Ni, Cu, Zn, or ceramic islands of these elements such as T1O2, NiO, Fe2C>3. , with an areal fraction of 5 - 50%, preferably at least 10%, more preferably at least 30%, using physical deposition, chemical deposition, electrochemical deposition, or ion implantation.

In further embodiments, a tunable hydrophilic TMD layer material is produced by using the following processing method: a DC or AC electric field is applied to the vertically arranged two electrodes, one above and one below the TMD layer with the applied electric field being at least 10 V/nm, preferably at least 30 V/nm to alter the semiconducting properties, with the bandgap widened by at least 5%, preferably at least 10%, and with the TMD made more hydrophilic with the water droplet contact angle to decrease by at least 5 degrees, preferably by at least 20 degrees for easier accommodation of fluidic chamber environment and improved adhesion of single enzyme molecule such as DNA or RNA polymerase. In certain embodiments, when the device is not in use, the device is evacuated and back-filled with inert gas so as to minimize inadvertent adhesion or adsorption of unwanted molecules. The devices disclosed herein may be used for whole genome sequences or to diagnose diseases, including but not limited to cancers.

In another aspect, a sequencing device is disclosed. The sequencing device includes an array of conducting electrode pairs, each pair of electrodes comprising a source and a drain electrode arrangement separated by a nanogap, the electrode array deposited and patterned on a dielectric substrate; at least one transition metal dichalcogenide (TMD) layer disposed on each pair of electrodes, wherein the TMD layer connects each source and drain electrode within each pair, and bridges each nanogap of each pair of electrodes; and a dielectric masking layer disposed on the TMD layer and comprising at least one opening that defines an exposed TMD region, wherein the at least one opening is sized so as to allow a single biomolecule to fit therein and to attach on to the exposed TMD region. In embodiments, at least one biomolecule is attached to the exposed TMD region. In embodiments, the at least one biomolecule comprises a polymerase enzyme. In embodiments, the sequencing device further includes a microfluidic system in fluid combination with the sequencing device to provide the at least one biomolecule. In embodiments, the TMD layer comprises MoS ₂ , WS ₂ , TiS ₂ , ZrS ₂ , HfS ₂ , VS ₂ , NbS ₂ , TaS ₂ , TcS ₂ , ReS ₂ , CoS ₂ , RhS ₂ , IrS ₂ , NiS ₂ , PdS ₂ , PtS ₂ , or any of their modifications or combinations, including modified stoichiometry of sulfur contents having MX _(2-X) or MX _(2+X) , wherein x is in the range of 0 - 1.0. In embodiments, the sulfur stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects so as to increase the surface energy and enhance the adhesion of the biomolecule to the exposed TMD region. In embodiments, the TMD layer comprises MoSe ₂ , WSe ₂ , TiSe ₂ , ZrSe ₂ , HfSe ₂ , VSe ₂ , NbSe ₂ , TaSe ₂ , TcSe ₂ , ReSe ₂ , CoSe ₂ , RhSe ₂ , IrSe ₂ , NiSe ₂ , PdSe ₂ , PtSe ₂ , or any of their modifications or combinations, including modified stoichiometry of selenium contents having MX _(2-X) or MX _(2+X) , wherein x is in the range of 0 - 1.0. In embodiments, the selenium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects in order to increase the surface energy of the TMD layer and enhance the adhesion of the biomolecule to the exposed TMD region. In embodiments, the TMD layer comprises MoTe ₂ , WTe ₂ , TiTe ₂ , ZrTe ₂ , HfTe ₂ , VTe ₂ , NbTe ₂ , TaTe ₂ , TcTe ₂ , ReTe ₂ , CoTe ₂ , RhTe ₂ , IrTe ₂ , NiTe ₂ , PdTe ₂ , PtTe ₂ , or any of their modifications or combinations, including modified stoichiometry of tellurium contents having MX( _2-X ) or MX( _2+X ), wherein x is in the range of 0 - 1.0. In embodiments, the tellurium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects in order to increase the surface energy of the TMD layer and enhance the adhesion of the biomolecule to the exposed TMD region. In embodiments, the TMD layer comprises Mo _x W _y Co _z )S ₂ or (Hf _x W _y Co _z )Te ₂ . In embodiments, the conducting electrode pairs comprise at least one of Au, Pt, Ag, Pd, Rh, or their alloys. In embodiments, the nanogap is about 2 nm to about 20 nm in length. In embodiments, the TMD layer comprises a defective TMD layer. In embodiments, the defective TMD layer comprises a linear nano-ribbon parallel array, a patterned shape nano- ribbon array, strained lattice defects, vacancies, interstitial defects, dislocation defects, foreign atom implanted defects, or nanoporous defects. In embodiments, the defective TMD layer comprises strained lattice defects, vacancies, interstitial defects, dislocation defects or foreign atom implanted defects with a defect density of at least about 10 ⁵ /cm ² . In embodiments, the defective TMD layer comprises nanoporous defects having an equivalent diameter of at least 2 nm with a defect density of at least lo cm ² . In embodiments, the defective TMD layer has a bandgap opened to a value of at least 0.2 eV.

In another aspect, a method of fabricating a sequencing device is disclosed. The method involves depositing and patteming an array of conducting electrode pairs on a dielectric substrate, each electrode paid defining a source and drain arrangement separated by a nanogap; depositing at least one TMD layer over each electrode pair; and nanopatterning a dielectric masking layer on the TMD layer. In embodiments, the method further involves processing the at least one TMD layer to obtain a defective TMD layer.

BRIEF DESCRIPTION OF THE DRAWINGS

The features and advantages of the embodiments of the present disclosure will become more apparent from the detailed description set forth below when taken in conjunction with the drawings. The drawings and the associated descriptions are provided to illustrate embodiments of the disclosure and not to limit the scope of what is claimed.

FIGS. 1A-1C illustrate example defects to be artificially introduced to a transition metal dichalcogenide (TMD) sheet such as M0S ₂ or WS ₂ , using various techniques to provide an increased bandgap or to provide many active site edge locations for strong adhesion of bridge structures or biomolecules (such as enzyme molecules). The TMD layer can be a single layer type or few layer type. FIG. 1A illustrates linear or zig-zag shape M0S ₂ or WS ₂ ribbon array; FIG. IB illustrates intentionally damaged surrounding area except for the linear ribbon regions; and FIG. 1C illustrates periodic or random defects;

FIGS. 2A and 2B illustrate example nanopatterning processes of TMD such as M0S ₂ or WS ₂ , using electron beam lithography (FIG. 2A) or nanoimprint lithography (FIG. 2B). In these embodiments, the TMD layer itself is physically reshaped into nanopatterns such as ribbons or islands. An alternative method is to intentionally damage the region of TMD outside the needed material area as shown in the previous figure, by using intentional disruption of crystal structure or lattice structure using e-beam, ion-beam, ion implantation, optical beam, and other radiations;

FIGS. 3A-3D illustrate an embodiment of fabrication of an exemplary molecular bridge of DNA or RNA sensor comprising size-limited, M0S ₂ islands (TMD islands in general), comprising depositing and patteming conducting electrode pair (source and drain) (FIG. 3A), placing a suspended M0S ₂ layer (FIG. 3B), adding a protective dielectric coating (FIG. 3C), allowing preferably a single molecule enzyme (polymerase) to attach onto the M0S ₂ , and enabling each of the polymerase reaction of nucleotide attachment (nucleotide monomers like A, T, C, G, U etc.) to change electrical properties of the molecular bridge for sequencing analysis (FIG. 3D);

FIG. 4 illustrates the top view of an array of TMD bridges like M0S ₂ or WS ₂ bridge molecular sensors, with the TMD positioned as a suspended layer or substrate-adhered layer. The enzyme polymerase molecule is shown only on the lower two electrode pairs. Massively parallel electronic sequencing analysis can be performed with many devices organized into a system, having as many as 10,000 or even at least 1 million devices;

FIGS. 5A-5D illustrate an embodiment of fabrication steps for an exemplary molecular bridge of DNA or RNA sensor comprising size-limited, M0S ₂ islands (TMD islands in general), comprising: depositing and patterning conducting electrode pairs (source and drain) (FIG. 5A), placing a suspended M0S ₂ layer (FIG. 5B), intentionally altering the TMD except the central masked regions by irradiation or doping to make it insulating or highly resistive (FIG. 5C), allowing preferably a single molecule enzyme (polymerase) to attach onto the M0S ₂ , and enable each of the polymerase reaction of nucleotide attachment (nucleotide monomers like A, T, C, G, U, etc.) to change electrical properties of the molecular bridge for sequencing analysis (FIG. 5D);

FIGS. 6A-6C illustrate exemplary embodiments of two configurations of TMD such as M0S ₂ or WS ₂ bridge placement as a suspended TMD bridge (FIG. 6A), and a substrate- adhered TMD bridge (FIG. 6B). A top view of the TMD bridge structure with attached polymerase enzyme is also shown in FIG. 6C. Top view shows that the single molecule enzyme (polymerase) on TMD enables each of the polymerase reaction of nucleotide attachment (nucleotide monomers like A, T, C, G, U, etc.) to change electrical properties of the molecular bridge for sequencing analysis;

FIGS. 7 A and 7B illustrate enzyme molecule connection to a TMD bridge via functional groups, with two resulting exemplary embodiments of a solid state molecular sensor, based on a suspended TMD bridge (FIG. 7A), and a substrate-adhered TMD bridge (FIG. 7B). Preferably a defective or porous TMD layer is utilized, which is masked to a limited size area (e.g., 2-20 nm) to enforce a single molecule attachment using a patterned dielectric coating (e.g., PMMA, PDMS or other adhesion-impeding polymer layer or S1O ₂ layer); FIGS. 8A and 8B illustrate embodiments of gated structure sequencing devices of TMD bridge like M0S ₂ or WS ₂ , with the gate electrode placed as parallel to the source and drain electrodes (FIG. 8A), or perpendicular to the nanogap spacing between the two (source and drain) electrodes (FIG. 8B). The tip of the gate electrode can also be placed above or below the nanogap;

FIG. 9 illustrates a top view of an array of TMD bridge molecular sensors like MoS ₂ or WS ₂ with the TMD positioned as a suspended layer or substrate-adhered layer. The enzyme polymerase molecule is shown only on the lowest electrode pair of the array. Massively parallel electronic sequencing analysis can be performed with many devices organized into a system, having as many as 10,000 or even at least 1 million devices;

FIGS. 10A-10B illustrate exemplary embodiments of two configurations of hydrophilic-enabled TMS bridge surface structures. The embodiment detailed in FIG. 10A comprises a hydrophilic TMS surface, either all of the TMD surface or preferably the exposed part of the TMD layer, is provided by (i) plasma treatment (e.g., with oxygen- containing plasma) to convert the hydrophobic surface of the TMD layer to a hydrophilic surface by imperfect crystallization (by at least 10%, preferably at least 30% area fraction of TMD surface material) of M0S ₂ type structure, e.g., by sulfurization/annealing at lower temp. The embodiment detailed in FIG. 10B comprises composite hydrophilic-hydrophobic configuration so as to enable easier biomolecule attachment and also allow other local covalent or hydrophobic-hydrophobic bonding. The size of either hydrophilic islands or hydrophobic islands is desirably 1-30 nm, preferably 1-10 nm, more preferably 1-5 nm, with the area fraction in the 85-15 ratio (or 15-85 ratio), preferably 70-30 ratio (or 30-70 ratio). The hydrophilic portion can be made by using masked plasma treatment or defective TMD layer (e.g., incomplete crystallization);

FIG. 11 illustrates a cross-sectional view of hydrophilicity-controllable TMD bridge molecular sensors like M0S ₂ or WS ₂ with the TMD positioned as a suspended layer (or, alternatively as substrate-adhered layer) and vertical electrodes to apply electric field to alter the semiconducting properties (to widen the bandgap) and make the TMD more hydrophilic for easier accommodation of fluidic chamber environment and improved adhesion of single enzyme molecule such as DNA or RNA polymerase. An array of these DNA or genome sequencing sensor can be made as a massively parallel sequencer system;

FIG. 12 illustrates an embodiment of a molecular bridge solid state sensor using nanogapped TMD layers for genome or DNA sequencing detection. Changes of current pulse shape and intensity or other signal aspects are measured upon attaching or detaching of a nucleotide or other biomolecules at the split-TMD tunnel junction configuration;

FIGS. 13A-13F illustrate exemplary fabrication steps for a nanopatterned TMD bridge using diblock copolymer mask. In FIG. 13 A, CVD grown, exfoliated or sulfurization activated TMD layer like M0S ₂ or WS ₂ on metal foil, forms the starting material. In FIG. 13B, after the metal is etched away, the TMD layer is transferred onto device surface, e.g., nano-gapped, Au, Pd or Pt electrode pair on S1O ₂ (or SiCVcoated Si substrate), to place the TMD layer as a suspended bridge. In FIG. 13C, TMD is covered by a thin layer of evaporated Si0 ₂ and a thin film of spin-coated block-copolymer PS-b-P4VP. In FIG. 13D, the PS-b- P4VP block-copolymer film is annealed and developed into a nanoscale two-phase structure, leaving the porous PS matrix as the template for subsequent patterning. In FIG. 13E, fluoride- based reactive ion etching (RIE) is used to penetrate and partem the S1O ₂ oxide layer, partially degrading the PS film, and to form the hard mask hole partem out of the thin S1O ₂ . In FIG. 13F, TMD layer in the exposed hole area is etched away by O ₂ plasma and then S1O ₂ is removed. Finally, nanoporous TMD on S1O ₂ is obtained, which is then pattemed into a size-limited island TMD by dielectric masking for single molecule (e.g., enzyme) attachment;

FIGS. 13G-13L illustrate an embodiment of AAO membrane based nanopatterning of TMD layer like M0S ₂ or WS ₂ for molecular bridge sensors for DNA sequencing. FIG. 13G depicts exfoliated, CVD or sulfurization grown M0S ₂ ; FIG. 13H depicts placement of M0S ₂ on substrate; FIG. 131 depicts AAO nanohole membrane fabricated; FIG. 13J depicts AAO placed on M0S2 surface; FIG. 13K depicts RIE etching of M0S2 through the AAO holes, and FIG. 13L depicts nano-patterned M0S ₂ on substrate obtained after AAO mask removal;

FIG. 13M is an image of exemplary patterning of M0S ₂ layer using AAO membrane to produce an 80 nm diameter hole array. The floating AAO membrane of FIG. 13G was collected onto the top surface of M0S ₂ layer coated S1O ₂ substrate, and the nanopatterning was conducted using BC¾/Ar plasma etching at 100 W under 4.5 mTorr for 4 min, with the AAO as the mask;

FIGS. 14A-14E illustrate an example evolution of mask layer being deposited on M0S ₂ ,e.g., by sputtering or evaporation. As shown in FIGS. 14A and 14B, at the early stage of deposition, the mask material can have a more defective structure. The nano-pinholes via incomplete deposition such as in FIG. 14B can be used as a mask through which the M0S ₂ can be etched to create nano-pinhole defects. As shown in FIGS. 14C and 14D, as the film gets thicker for longer period deposition, the pinholes or defects gradually gets less frequent. As shown in FIG. 14E, the incompletely deposited mask material in FIG. 14B is utilized to form nano-pinhole defects in M0S ₂ . The mask material is then removed by chemical or plasma etch.

FIGS. 15A-15D illustrate exemplary perforated and defective TMD like MoS ₂ or WS ₂ for molecular bridge DNA or RNA sensors and method for making sensors. FIG. 15A depicts a TMD layer on dielectric substrate starting material; FIG. 15B depicts coating the TMD surface with metallic nano-islands of 1-20 nm size; FIG. 15C depicts inducing diffusional reactions by heating to form altered composition defects, or nanopores in the TMD layer by differential chemical etching or RIE etching; and FIG. 15D depicts adding electrical lead wires and size-limiting dielectric layer (polymer or ceramic) to make the solid state electronic sensor for single enzyme molecule attachment and associated analytes attachment and sequencing analysis;

FIGS. 16A-16D illustrate defective TMD like MoS ₂ or WS ₂ by a beam irradiation for enhanced molecular bridge DNA or RNA sensors. FIG. 16A depicts placing a TMD layer; FIG. 16B depicts irradiating TMD with ion implantation beam, plasma reactive ion etch (RIE) atmosphere, broadened optical, electron, ion or neutron beam; FIG. 16C depicts inducing defective TMD (with optional addition of post-irradiation annealing); and FIG. 16D depicts adding electrical lead wires and size-limiting dielectric mask layer (polymer or ceramic) to make the solid state electronic sensor for single enzyme molecule and associated analytes attachment and sequencing analysis. The desired density of defects in TMD layer like MoS ₂ or WS ₂ is at least 10 ⁵ /cm ² , preferably at least 10 ⁷ /cm ² ;

FIGS. 17A-17D illustrate chemically induced defective TMD like MoS ₂ or WS ₂ (disturbed lattice regions or nanopores). FIG. 17A depicts s TMD layer; FIG. 17B depicts chemical etching of TMD surface; FIG. 17C depicts defective TMD (with optional addition of post-etch annealing); and FIG. 17D depicts adding electrical lead wires and size-limiting dielectric layer (polymer or ceramic) to make the solid state molecular electronic sensor for single enzyme molecule and associated analytes attachment and sequencing analysis;

FIGS. 18A-18D illustrate a shape-altered TMD layer induced by a shape-altering dielectric insert within or near the nanogap. Such a shape-altering insert serves to provide additional defects for enhanced biomolecule adhesion, which can be left permanently underneath the TMD layer as a mechanical support, or dissolved away;

FIG. 19 illustrates an embodiment of a massively parallel array of solid state molecular sensor device comprising many TMD-containing enzyme polymerase structures (e.g., with M0S2 or WS2 layer) for DNA or genome sequencing. An areal distribution of the devices with associate routing of electrical wiring is provided;

FIG. 20 illustrates an embodiment of a microfluidic chamber into which enzyme or other biomolecules are supplied in a phosphate-buffered saline (PBS) or other liquid solutions. Individual single enzyme molecules are selectively attached with a high probability onto each of the size-limited, exposed TMD island regions (e.g., MoS ₂ or WS2 layer) on the massively parallel sensor array. The unused biomolecules which did not adhere to the TMD islands are washed away out of the fluidic chamber. The analytes to be detected such as nucleotides or proteins are then supplied into the chamber to attach to the enzyme polymerase to induce electrical signal pulse for sequencing analysis;

FIG. 21 illustrates an exemplary sequential interrogation of electrodes from the TMD- containing enzyme polymerase molecular sensor (e.g., with M0S2 or WS2 layer) for DNA or genome sequencing by using a common lead wire on one side of the array;

FIGS. 22A-22B illustrate an exemplary three-dimensional array of molecular electronics genome-sequencing platform comprising TMD-based enzyme polymerase structure, e.g., with M0S2 or WS2 layer. An electrically insulating top coating (not shown) such as polymer or oxide layer (e.g., AI2O ₃ , S1O2, etc.) is applied except the exposed TMD region having enzyme polymerase structure for nucleotide attachment. FIG. 22A depicts a two-dimensional molecular electronics genome-sequencing device array is separately packaged into an individual microfluidic system, with each of the microfluidic layer stacked into a three-dimensional system, FIG. 22B depicts a two-dimensional molecular electronics genome-sequencing device arrays are stacked into three dimensional configuration but are housed in a single microfluidic system. The total number of molecular sensors can be at least 1,000, and can be as many as 1 million or more for massive parallel genome sequencing analysis; and

FIG. 23 illustrates a block diagram flowchart of DNA or genome sequencing system comprising TMD such as M0S2 or WS2 and enzyme polymerase sensor array, microfluidic structures, signal detection electronic circuits and associated devices, data analysis, storage or transmission devices, as well as applications of the sequencing devices for control, cure or prevention of diseases.

It is to be understood that the drawings are for purposes of illustrating the concepts of the embodiments disclosed herein and are not to scale. DETAILED DESCRIPTION

In an aspect, a new improved sequencing apparatus, structures, and methods using two-dimensional, layer structured semiconductors which provide reliable DNA and genome analysis performance and are amenable to scalable manufacturing are disclosed.

Two dimensional (2D) layered materials such as transition metal dichalcogenides

(TMDs) materials and devices have received attention by virtue of their unique electronic, physical and chemical properties. An example is molybdenum dichalcogenide M0S ₂ which can be incorporated as a sensor device. M0S ₂ type 2D materials can be a single layered material or several layered material. The 2D layer materials such as M0S ₂ can be produced by various known techniques, e.g., by isolation of very thin M0S ₂ layer through mechanical exfoliation, physical or chemical vapor deposition, molecular beam epitaxy (MBE) type construction, or sulfurization of a transition metal layer such as Mo or W.

Definitions

As used herein, "bandgap" means the energy range in a solid in which electrons do not exist.

As used herein, "nano-pinhole defects" means through-hole defects with a diameter typically less than about 10 nm, which are formed during incomplete deposition of thin films. The nano-pinhole defects can be present in a mono atomic layer or a multi atomic layer, and can be configured as vertical holes or inclined holes having a circular, oval or irregular shape,

As used herein, "nucleotide" means either the native dNTPs like A, T, C, G (i.e., dATP, dTTP, dCTP and dGTP), or collectively refers to various types of modified dNTPs as described above.

As used herein, "polymerase" means an enzyme that synthesizes long chains or polymers of nucleic acids. For example, DNA polymerase and RNA polymerase can copy a DNA or RNA template strand, respectively, using base-pairing interactions, which is utilized to assemble DNA and RNA molecules.

As used herein, "stoichiometry" means the relative quantities of elements in a compound.

As used herein, "van der Waals" means a residual attractive force between molecules or atomic groups that are the result of covalent or electrostatic interactions. TMD layers and combined TMD materials for sensor bridges

In some embodiments, a TMD layer is incorporated as a part of sensor bridge structure to attach an enzyme type biomolecule to attract various types of nucleotides for electronic detection signals.

Two dimensional transition metal dichalcogenide (TMD) monolayers are in general atomically thin semiconductors of the type MX ₂ , with M a transition metal atom (notably including Mo, W, or Ti, Zr, Hf, V, Nb, Ta, Tc, Re, Co, Rh, Ir, Ni, Pd, Pt) and X a chalcogen atom (such as S, Se, or Te.). One layer of M atoms is sandwiched between two layers of X atoms. Both the transition metal and the chalcogenide element can be partly replaced (or doped) with other elements. Therefore, the two dimensional TMD layer incorporated into the molecular sensor bridge construction can have various modified or altered composition ranges, including the following;

(l) MoS ₂ , WS ₂ , or TiS ₂ , ZrS ₂ , HfS ₂ , VS ₂ , NbS ₂ , TaS ₂ , TcS ₂ , ReS ₂ , CoS ₂ , RhS ₂ , IrS ₂ , NiS ₂ , PdS ₂ , PtS ₂ and their modifications or combinations, including modified stoichiometry of sulfur contents having MX _(2-X) or MX _(2+X) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. For some embodiments, the sulfur stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects so as to increase the surface energy and enhance the adhesion of biomolecule to the bridge sensor. Such defects can also increase the bandgap for stronger sensor signals;

(ii) MoSe ₂ , WSe ₂ , or TiSe ₂ , ZrSe ₂ , HfSe ₂ , VSe ₂ , NbSe ₂ , TaSe ₂ , TcSe ₂ , ReSe ₂ , CoSe ₂ , RhSe ₂ , IrSe ₂ , NiSe ₂ , PdSe ₂ , PtSe ₂ and their modifications or combinations, including modified stoichiometry of selenium contents having MX _(2-X) or MX _(2+X) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. For some embodiments, the selenium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects so as to increase the surface energy and enhance the adhesion of biomolecule to the bridge sensor. Such defects can also increase the bandgap for stronger sensor signals;

(iii) MoTe ₂ , WTe ₂ , or TiTe ₂ , ZrTe ₂ , HfTe ₂ , VTe ₂ , NbTe ₂ , TaTe ₂ , TcTe ₂ , ReTe ₂ , CoTe ₂ , RhTe ₂ , IrTe ₂ , NiTe ₂ , PdTe ₂ , PtTe ₂ and their modifications or combinations, including modified stoichiometry of tellurium contents having MX _(2-X) or MX _(2+X) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. For some embodiments, the tellurium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects so as to increase the surface energy and enhance the adhesion of biomolecule to the bridge sensor. Such defects can also increase the bandgap for stronger sensor signals;

(iv) Mixed TMD compounds in which the MX ₂ compound has mixed metals and/or mixed chalcogenide. For example Mo(S _x SeyTe _z )2, W(S _x SeyTe _z )2, or Ti(S _x SeyTe _z )2,

Zr(S _x Se _y Te _z ) ₂ , Hf(S _x Se _y Te _z ) ₂ , V(S _x Se _y Te _z ) ₂ , Nb(S _x Se _y Te _z ) ₂ , Ta(S _x Se _y Te _z ) ₂ , Tc(S _x Se _y Te _z ) ₂ , Re(S _x Se _y Te _z ) ₂ , Co(S _x Se _y Te _z ) ₂ , Rh(S _x Se _y Te _z ) ₂ , Ir(S _x Se _y Te _z ) ₂ , Ni(S _x Se _y Te _z ) ₂ , Pd(S _x Se _y Te _z ) ₂ , Pt(S _x Se _y Te _z ) ₂ where the combined (x + y + z) is 1 - 3, preferably 0.5 - 1.5, even more preferably 0.7 - 1.3. Alternatively two or more metals can be combined for sulfur containing, Se-containing or Te-containing TMD layers, e.g., (Mo _x W _y Co _z )S ₂ , (Hf _x W _y Co _z )Te ₂ and so forth; or

(v) M(i _-W )NyX( _2-Z )Y _z structure in which the transition metal M is partially substituted with non-transition elements N, with a concentration of w and the N element selected from one or more of Al, Si, Ga, Ge, In, Sn, Sb, Bi, Al, Na, K, Ca, Mg, Sr, Ba, with the w value in the range of 0-0.3, and the chalcogenide element X partially substituted with a non- chalcogenide element Y, with the Y element selected from one or more of Li, B, C, N, O, P, F, CI, I, with the z value in the range of 0 - 0.3.

As the intentionally induced defects in the TMD layers of (i) to (v) described above enhances the biomolecule adhesion and sensor signal, the adhesion of biomolecule such as enzyme polymerase to the sensor bridge, is improved by using such intentionally defective TMD layer, with the probability and frequency of reliable and robust biomolecule increased by at least 20%, preferably at least 50%, even more preferably by at least 100%.

Typical thickness of a MoS ₂ monolayer is 6.5A. These TMD materials in their simplest monolayer structure, e.g., MoS ₂ , WS ₂ , MoSe ₂ , WSe ₂ , MoTe ₂ , have a direct band gap, and hence can be used in electronics as transistors or sensors. Either monolayer TMD or few layer TMD can be structurally modified, to be utilized as solid state DNA or genome sensors, without labeling with optical capability. Being an ultrathin direct bandgap semiconductor, a transition metal dichalcogenide such as single-layer MoS ₂ has found some useful applications in nanoelectronics, optoelectronics, and energy harvesting. However, not many sensor applications have been attempted or demonstrated with proper characteristics, especially for DNA or genome sequencing purposes.

Disclosed herein are label-free DNA or RNA sequencing device structures utilizing a TMD-based frame with an enzyme polymerase for detection of electronic signals when an individual nucleotide is attached onto a nucleic acid template. In some embodiments, two dimensional semiconductors of processed, defective or nanoporous Transition Metal Dichalcogenide (TMD) layer material are employed so as to utilize altered bandgaps of the TMD layer and enhanced attachment of single biomolecules. In some embodiments, the defective-TMD-based sequencing systems invented here can be assembled into a massively parallel configuration for rapid analysis of targets including nucleotides, in particular for applications of sequencing of a DNA molecule, or a collection of such molecules constituting an entire genome. Devices

In some embodiments, a sequencing device is provided comprising: (a) an electrode array of conducting electrode pairs, each pair of electrodes comprising a source and a drain electrode separated by a nanogap, said electrode array deposited and patterned on a dielectric substrate; (b) a single-layer or few-layer thick transition metal dichalcogenide (TMD) layer disposed on each pair of electrodes, connecting each source and drain electrode within each pair, and bridging each nanogap of each pair; (c) a dielectric masking layer disposed on the TMD layer and comprising size-limited openings that define exposed TMD regions, each opening sized so as to allow only a single enzyme biomolecule to fit therein and to attach onto the exposed TMD region defined by each opening; (d) an enzyme molecule attached to each exposed TMD region such that only one enzyme molecule is found within each opening; and (d) a microfluidic system encasing the electrode array, wherein attachment or detachment of a biomolecule selected from the group consisting of a nucleotide monomer, a protein, and a DNA segment, onto the enzyme molecule, one at a time, can be monitored as a uniquely identifiable electrical signal pulse to determine the specific nature of the biomolecule attaching or detaching.

In some embodiments, the dielectric substrate comprises Si0 ₂ . In some embodiments, the dielectric substrate comprises AI2O ₃ .

In some embodiments, the TMD is selected from MoS ₂ , WS ₂ , TiS ₂ , ZrS ₂ , HfS ₂ , VS ₂ , NbS ₂ , TaS ₂ , TcS ₂ , ReS ₂ , CoS ₂ , RhS ₂ , IrS ₂ , NiS ₂ , PdS ₂ , PtS ₂ and their modifications or combinations. In some embodiments, the TMD is MoS ₂ . In some embodiments, the TMD is WS ₂

In some embodiments, the TMD is selected from MoS ₂ , WS ₂ , TiS ₂ , ZrS ₂ , HfS ₂ , VS ₂ , NbS ₂ , TaS ₂ , TcS ₂ , ReS ₂ , CoS ₂ , RhS ₂ , IrS ₂ , NiS ₂ , PdS ₂ , PtS ₂ and their modifications or combinations, including modified stoichiometry of sulfur contents having MX _(2-X) or MX _(2+X) wherein x is in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. In some embodiments, the TMD is selected from MoS ₂ , WS ₂ , TiS ₂ , ZrS ₂ , HfS ₂ , VS ₂ , NbS ₂ , TaS ₂ , TcS ₂ , ReS ₂ , CoS ₂ , RhS ₂ , IrS ₂ , NiS ₂ , PdS ₂ , PtS ₂ and their modifications or combinations and the stoichiometry of sulfur is not modified.

In some embodiments, the TMD layer comprises defects. In some embodiments, the defects are vacancy defects. In some embodiments, the defects are interstitial defects. In some embodiments, the defects are nano-pinhole pores. In some embodiments, the defects are aggregated defects so as to increase the surface energy and enhance the adhesion of the biomolecule to the bridge sensor, increasing the bandgap for stronger electrical signal pulse.

In some embodiments, the sulfur stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, nano-pinhole defects and aggregated defects so as to increase the surface energy and enhance the adhesion of the biomolecule to the bridge sensor, increasing the bandgap for stronger electrical signal pulse.

In some embodiments, the TMD is selected from MoSe ₂ , WSe ₂ , or TiSe ₂ , ZrSe ₂ ,

HfSe ₂ , VSe ₂ , NbSe ₂ , TaSe ₂ , TcSe ₂ , ReSe ₂ , CoSe ₂ , RhSe ₂ , IrSe ₂ , NiSe ₂ , PdSe ₂ , PtSe ₂ and their modifications or combinations, including modified stoichiometry of selenium contents having MX _(2-X) or MX _(2+X) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. In some embodiments, the TMD is selected from MoSe ₂ , WSe ₂ , or TiSe ₂ , ZrSe ₂ , HfSe ₂ , VSe ₂ , NbSe ₂ , TaSe ₂ , TcSe ₂ , ReSe ₂ , CoSe ₂ , RhSe ₂ , IrSe ₂ , NiSe ₂ , PdSe ₂ , PtSe ₂ and their modifications or combinations and the stoichiometry of selenium is not modified.

In some embodiments, defects are artificially introduced into TMD. In some embodiments, the defects are introduced to increase bandgap. In some embodiments, the defects are introduced to provide active site edge locations for strong adhesion of bridge structures or biomolecules such as enzyme molecules.

In some embodiments, TMD is selected from MoTe ₂ , WTe ₂ , or TiTe ₂ , ZrTe ₂ , HfTe ₂ , VTe ₂ , NbTe ₂ , TaTe ₂ , TcTe ₂ , ReTe ₂ , CoTe ₂ , RhTe ₂ , IrTe ₂ , NiTe ₂ , PdTe ₂ , PtTe ₂ and their modifications or combinations.

In some embodiments, TMD is selected from MoTe ₂ , WTe ₂ , or TiTe ₂ , ZrTe ₂ , HfTe ₂ ,

VTe ₂ , NbTe ₂ , TaTe ₂ , TcTe ₂ , ReTe ₂ , CoTe ₂ , RhTe ₂ , IrTe ₂ , NiTe ₂ , PdTe ₂ , PtTe ₂ and their modifications or combinations, including modified stoichiometry of Tellurium contents having MX _(2-X) or MX _(2+X) with the desired value of x in the range of 0 - 1.0, preferably in the range of 0 - 0.5, even more preferably 0 - 0.3. In some embodiments, TMD is selected from MoTe ₂ , WTe ₂ , or TiTe ₂ , ZrTe ₂ , HfTe ₂ , VTe ₂ , NbTe ₂ , TaTe ₂ , TcTe ₂ , ReTe ₂ , CoTe ₂ , RhTe ₂ , IrTe ₂ , NiTe ₂ , PdTe ₂ , PtTe ₂ and their modifications or combinations and the stoichiometry of tellurium is not modified.

In some embodiments, the tellurium stoichiometry is intentionally altered so as to provide vacancy defects, interstitial defects, and aggregated defects in order to increase the surface energy of the TMD layer and enhance the adhesion of biomolecule to the bridge sensor for stronger sensor signals.

In some embodiments, the TMD comprises a mixed TMD selected from TMD compounds in which the MX ₂ compound has mixed metals and/or mixed chalcogenide, selected from the group consisting of Mo(S _x Se _y Te _z ) ₂ , W(S _x Se _y Te _z ) ₂ , Ti(S _x Se _y Te _z ) ₂ , Zr(S _x Se _y Te _z ) ₂ , Hf(S _x SeyTe _z ) ₂ , V(S _x SeyTe _z ) ₂ , Nb(S _x SeyTe _z ) ₂ , Ta(S _x SeyTe _z ) ₂ ,

Re(S _x Se _y Te _z ) ₂ , Co(S _x Se _y Te _z ) ₂ , Rh(S _x Se _y Te _z ) ₂ , Ir(S _x Se _y Te _z ) ₂ , Ni(S _x Se _y Te _z ) ₂ , Pd(S _x Se _y Te _z ) ₂ , and Pt(S _x Se _y Te _z ) ₂ wherein the combined (x + y + z) is 1 - 3, 0.5 - 1.5, or 0.7 - 1.3.

In some embodiments, two or more metals are combined for sulfur containing, Se- containing or Te-containing TMD layers.

In some embodiments, the TMD layer comprises Mo _x W _y Co _z )S ₂ or (Hf _x W _y Co _z )Te ₂ . In some embodiments, the TMD comprises a M ₍ i _-W) N _y X _(2-Z) Y _z structure in which the transition metal M is partially substituted with non-transition elements N, with a concentration of w and the N element selected from one or more of Al, Si, Ga, Ge, In, Sn, Sb, Bi, Al, Na, K, Ca, Mg, Sr, Ba, with the w value in the range of 0 - 0.3, and the chalcogenide element X partially substituted with a non-chalcogenide element Y, with the Y element selected from one or more of Li, B, C, N, O, P, F, CI, I, with the z value in the range of 0 - 0.3. In some embodiments, the w value is greater than 0.3, for example, greater than 0.4, greater than 0.5, greater than 0.6, greater than 0.7, greater than 0.8, greater than 0.9, or greater than 1.0. In some embodiments, the z value is greater than 0.3, for example, greater than 0.4, greater than 0.5, greater than 0.6, greater than 0.7, greater than 0.8, greater than 0.9, or greater than 1.0.

In some embodiments, the metallic conducting electrode pair is selected from Au, Pt, Ag, Pd, Rh, or their alloys.

In some embodiments, the nanogap is 2-20 nm. In some embodiments, the nanogap is less than 2 nm, for example less than 1.5 nm, less than 1.0 nm, or less than 0.5 nm. In some embodiments, the nanogap is greater than 20 nm, for example, greater than 25 nm, greater than 30 nm, greater than 35 nm, greater than 40 nm, greater than 45 nm, or greater than 50 nm.

In some embodiments, the size-limited openings are preferably less than 30 nm average equivalent diameter each, more preferably less than 20 nm equivalent diameter, even more preferably less than 10 nm equivalent diameter, by lithographically defined coverage of dielectric material layer of polymer or ceramic outside a specific region intended for attaching only a single molecule. In some embodiments, the size-limited openings are greater than 30 nm, for example, greater than 35 nm, greater than 40 nm, greater than 45 nm, or greater than 50 nm.

In some embodiments, the size-limited openings are 30 nm equivalent diameter each, or 20 nm equivalent diameter each, or 10 nm equivalent diameter each, and wherein: (i) the TMD layer comprises an intentionally damaged structure with insulator or very high resistivity characteristics serving as the mask material to enable single molecule attachment; (i) with at least 100 ohm-cm, preferably at least 10,000 ohm-cm, even more preferably at least 1 mega ohm-cm resistivity for the regions outside a specific region intended for attaching only a single molecule; and (ii) with the intentional damaging performed by electron bombardment, laser radiation bombardment, ion bombardment, or ion implant doping.

In some embodiments, the size-limited openings are less than 10 nm equivalent diameter each and wherein: (i) the TMD layer comprises an intentionally damaged structure with insulator or very high resistivity characteristics serving as the mask material to enable single molecule attachment; (i) with at least 100 ohm-cm, preferably at least 10,000 ohm-cm, even more preferably at least 1 mega ohm-cm resistivity for the regions outside a specific region intended for attaching only a single molecule; and (ii) with the intentional damaging performed by electron bombardment, laser radiation bombardment, ion bombardment, or ion implant doping.

In some embodiments, the size-limited openings are greater than 30 nm equivalent diameter each and wherein: (i) the TMD layer comprises an intentionally damaged structure with insulator or very high resistivity characteristics serving as the mask material to enable single molecule attachment; (i) with at least 100 ohm-cm, preferably at least 10,000 ohm-cm, even more preferably at least 1 mega ohm-cm resistivity for the regions outside a specific region intended for attaching only a single molecule; and (ii) with the intentional damaging performed by electron bombardment, laser radiation bombardment, ion bombardment, or ion implant doping.

In some embodiments, the resistivity for the regions outside a specific region intended for attaching only a single molecule of any of the devices disclosed herein is greater than 1 mega ohm-cm resistivity, for example, greater than 1.5 mega ohm-cm resistivity, greater than 2.0 mega ohm-cm resistivity, greater than 2.5 mega ohm-cm resistivity, greater than 3.0 mega ohm-cm resistivity, greater than 3.5 mega ohm-cm resistivity, greater than 4.0 mega ohm-cm resistivity, greater than 4.5 mega ohm-cm resistivity, or greater than 5.0 mega ohm-cm resistivity.

In some embodiments, the TMD layer is defective with the defects selected from linear nano-ribbon parallel array, patterned shape nano-ribbon array, strained lattice defects, vacancies, interstitial defects, dislocation defects, foreign atom implanted defects, nano- pinhole defects or nanoporous defects.

In some embodiments, the size-limited TMD layer contains strained lattice defects, vacancies, interstitial defects, dislocation defects or foreign atom implanted defects with a defect density of at least 10 ⁵ /cm ² . In some embodiments, the defect density is greater than 10 /cm , for example, greater than 10 /cm , greater than 10 /cm , greater than 10 /cm , greater than 10 ⁹ /cm ² , or greater than 10 ¹⁰ /cm ² .

In some embodiments, the defects in the TMD layer are nanoporous defects or nano- pinhole defects having an equivalent diameter of at least 2 nm with a defect density of at least lo cm ² . In some embodiments, the defect density is greater than lo cm ² , for example, greater than 10 4 /cm 2 , greater than 105 /cm 2 , greater than 106 /cm 2 , greater than 107 /cm2 , or greater than 10 ⁸ /cm ² .

In some embodiments, the TMD layer is defective with the bandgap opened additionally by at least 0.2 eV, preferably by at least 0.5 eV compared to the TMD without defects. In some embodiments, the TMD layer is defective with the bandgap opened additionally by greater than 0.5 eV, for example, greater than 0.6 eV, greater than 0.7 eV, greater than 0.8 eV, greater than 0.9 eV, greater than 1.0 eV, greater than 1.1 eV, greater than 1.2 eV, greater than 1.3 eV, greater than 1.4 eV, greater than 1.5 eV, greater than 1.6 eV, greater than 1.7 eV, greater than 1.8 eV, greater than 1.9 eV, or greater than 2.0 eV.

In some embodiments, the TMD layer surface exhibits hydrophilic characteristics; (i) with the hydrophilic area having a water droplet contact angle of at most 50 degrees, preferably at most 30 degrees, even more preferably at most 15 degrees; (ii) with an improved biomolecule attachment frequency with the adhesion improvement by at least 30%, preferably by at least 50%, even more preferably by at least 100% increased adhesion event as compared to the all hydrophobic TMD surface during microfluidic chamber processing of fluid supplying to provide biomolecules, nucleotides, and related biological or chemical components, as well as washing or fluid replacement operations; and (iii) the hydrophilic characteristics is associated with defects including strained lattice, vacancies, interstitials, dislocations, nanopores, foreign atom doping, with the defect density being at least loVcm ² , preferably at least 10 ⁵ /cm ² . In some embodiments, the hydrophilic area has a water droplet contact angle of less than 15 degrees, for example, less than 14 degrees, less than 13 degrees, less than 12 degrees, less than 11 degrees, less than 10 degrees, less than 9 degrees, less than 8 degrees, less than 7 degrees, less than 6 degrees, or less than 5 degrees.

In some embodiments, the improved biomolecule attachment frequency has an adhesion improvement greater than 75%, for example, greater than 80%, greater than 85%, greater than 90%, greater than 95%, greater than 96%, greater than 97%, greater than 98%, greater than 99%, greater than 99.9%, greater than 99.99%, greater than 99.999%, or greater than 99.9999%. In some embodiments, the defect density is greater than 10 ⁵ /cm2, for example, greater than 10 ⁶ /cm2, greater than 10 ⁷ /cm2, greater than 10 ⁸ /cm2, greater than 109/cm2, or greater than 10 ¹⁰ /cm2.

In some embodiments, the TMD layer surface consists of a mixed structure of a hydrophilic region and a hydrophobic region, and (i) the hydrophilic area has a water droplet contact angle of at most 50 degrees, preferably at most 30 degrees, even more preferably at most 15 degrees; (ii) the area fraction of hydrophilic region is at least 10%, preferably at least 30%, even more preferably at least 50% area fraction of the exposed TMD surface to attract a single biomolecule; (iii) the hydrophilic regions are in the form of circular, oval, rectangular, or irregular islands, or in a striped configuration; (iv) the TMD surface having defects such as vacancies, interstitials, dislocations or aggregated defects, nanopores, chemically doped regions with foreign atoms, or striped pores, with the density of such defects being at least lO cm ² , preferably at least 10 ⁵ /cm ² ; (v) such a composite hydrophilic-hydrophobic configuration enables improved biomolecule attachment frequency with the adhesion improvement by at least 30%, preferably by at least 50%, even more preferably by at least 100% increased adhesion event as compared to the all hydrophobic TMD surface during microfluidic chamber processing of fluid supplying to provide biomolecules, nucleotides, and related biological or chemical components, as well as washing or fluid replacement operations; and (vi) the size of either hydrophilic islands or hydrophobic islands is desirably 1 -30 nm, preferably 1 -10 nm, more preferably 1 -5 nm.

In some embodiments, the water droplet contact angle is less than 15 degrees, for example, less than 14 degrees, less than 13 degrees, less than 12 degrees, less than 11 degrees, less than 10 degrees, less than 9 degrees, less than 8 degrees, less than 7 degrees, less than 6 degrees, or less than 5 degrees. In some embodiments, the area fraction of the hydrophilic region is greater than 50% of the area fraction of the exposed TMD surface, for example, greater than 55%, greater than 60% percent, greater than 65%, greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, or greater than 95%. In some embodiments, the defect density is greater than 10 ⁵ /cm2, for example, greater than 10 ⁶ /cm2, greater than 10 ⁷ /cm2, greater than 10 ⁸ /cm2, greater than 10 ⁹ /cm2, or greater than 10 ¹⁰ /cm2.

In some embodiments, the TMD layer has tunable hydrophilicity, wherein: (i) the TMD layer is either suspended between two electrodes or fixed on top of two electrodes without suspended structural configuration; (ii) the TMD bridge surface is size-limited for attachment of single biomolecule; (iii) on-demand switching of hydrophobic to hydrophilic surface state is enabled by a device configuration of at least a pair of vertical electrodes positioned below and above the sensor bridge structure so as to apply electric field of at least 10 V/nm, preferably at least 30 V/nm to alter the semiconducting properties and widen the bandgap by at least 5%, preferably at least 10%, and make the TMD more hydrophilic with the water droplet contact angle to decrease by at least 5 degrees, preferably by at least 20 degrees for easier accommodation of microfluidic chamber environment and improved adhesion probability of single enzyme molecule such as DNA or RNA polymerase increasing by at least 30%; (iv) the electric field applied is a DC electric field or AC electric field; (v) the hydrophilic improvement is capable of being reversed to return to hydrophobic state to enable a release of previously used biomolecule and to avoid unnecessary attachment of biomolecules; and (vi) optionally having at least 1 ,000, preferably as many as 10,000 or even more preferably at least 1 million devices, with one or more selected electrode-paired devices simultaneously or in a series operation tunable to be hydrophilic or hydrophobic.

In some embodiments, the electric field is greater than 30 V/nm, for example, greater than 35 V/nm, greater than 40 V/nm, greater than 45 V/nm, or greater than 50 V/nm. In some embodiments, the bandgap is widened by greater than 10%, for example, greater than 15%, greater than 20%, greater than 25%, greater than 30%, greater than 35%, greater than 40%, greater than 45%, or greater than 50%.

In some embodiments, the biomolecule to be attached onto the TMD is an enzyme polymerase molecule. In some embodiments, the polymerase molecule is a RNA polymerase. In some embodiments, the polymerase molecule is a DNA polymerase.

In some embodiments, the biomolecule to be attached onto the TMD is selected from various other biopolymers of DNA, RNA, proteins, ribozyme, aptamer or polysaccharide.

In some embodiments, the two-dimensional shaped TMD layer is locally converted to three-dimensionally shaped TMD, so as to provide mechanical support for robust and reliable TMD positioning, with additional defects at the curved or kinked position with displaced or strained lattice in TMD, to produce higher-energy-state positions for enhanced adhesion of enzyme biomolecules, with the altered shape TMD having the following structural characteristics of; (i) an introduction of new modes of defects and shape discontinuity for higher-energy -state local regions; (ii) a shape-altering insert structure made of dielectric material selected from polymer materials or ceramics materials; (iii) the shape-altering insert structure having a uniformly or non-uniformly protruding structure beyond the level of metallic conductor electrode top surface so as to make the TMD layer non-flat geometry selected the configuration of being bent, curvatured, dome-shaped, irregular-shaped, buckled, or locally punctured shape and introduce displaced; (iv) the shape-altered TMD layer already possessing a defective structure comprising lattice defects of strained lattice, vacancies, interstitials, dislocations, nanopores, chemically doped regions with a defect density of at least lO cm ² ; (v) the altered shape selected from hemispherical, rectangle, oval, wavy, or other periodic or irregular geometry; and (vi) the shape-altering insert permanently left underneath the TMD layer to serve as a beneficial mechanical support to guard against mechanical detachment or damage of the TMD layer during microfluidic handling of the sequencing device systems and associated inadvertent force applied to the suspended or barely bonded TMD layer on the nanogap region, or etched away to leave a mechanically compliant, protruding TMD layer.

In some embodiments, the TMD layer is in contact with the dielectric substrate with no nanogap, with a pair of metallic electrodes extended from the both ends of the TMD island as electric lead wires.

In some embodiments, the enzyme polymerase molecule connection to the TMD surface is via functional groups or functional group pairs selected from a list of streptavidin- biotin pair, antigen-antibody interaction, bifunctional ligands using mercaptocarbonic acids [HS-(CH ₂ )«-COOH, » = 1-15], peptide functional groups, thiol-alkyne pair, COOH-NH ₂ functional group pair, a thiol-maleimide azide pair, silanization linkage using mercaptosilane compounds, and a NHS (N-hydroxysuccinimide) ester-amine pair.

In some embodiments, the dNTP nucleotide being attached to the enzyme polymerase molecule is a modified nucleotide type to enhance the incorporation signals, or produce signals with enhanced differences between the different bases (A, C, G, T) incorporation events, for greater accuracy determining the template sequence, with such dNTP modifications include modifications of; (i). the base, such as 7-deaza forms, 8-bromo forms; (ii) the alpha- and beta- phosphates, such as thiolated forms or bromated forms of these phosphates; (iii) the gamma-phosphate modifications, including the addition of phosphates, such as tetra-, penta- or hexa- phosphates forms; or (iv) the groups added to the terminal phosphate.

In some embodiments, the electrode arrangement comprises a triode configuration with a gate electrode placed parallel to each of said source and drain electrodes or perpendicular to each nanogap between each of source and drain electrodes in the electrode array.

In some embodiments, the electrodes, TMD layer, masking dielectric, and enzyme molecule are arranged into an array configuration so as to allow massively parallel electronic sequencing analysis using devices organized into a system having at least 1,000, preferably at least 1 million devices. In some embodiments the system as greater than 1 million devices, for example, greater than 2 million devices, greater than 3 million devices, greater than 4 million devices, greater than 5 million devices, greater than 6 million devices, greater than 7 million devices, greater than 8 million devices, greater than 9 million devices, or greater than 10 million devices.

In some embodiments, a sequential interrogation of an array of electrodes in the TMD-containing enzyme polymerase molecular sensor is enabled for DNA or genome sequencing by using a common lead wire on one side of the array.

In some embodiments, the electrodes, TMD layer, masking dielectric, and enzyme molecule are arranged into a three-dimensional array of molecular electronics genome- sequencing platform using a stacked microfluidic chamber or a common microfluidic chamber for a stacked layer devices, so as to allow massively parallel electronic sequencing analysis using devices organized into a system having at least 1 ,000, preferably at least 1 million devices.

Methods

In some embodiments, a method of fabricating a TMD based DNA or genome sequencing device is provided, said method comprising: (a) providing an array of metallic conducting electrode pairs with a source and drain arrangement deposited and patterned on a dielectric substrate; (b) depositing a single-layer or few-layer TMD by using a liquid container lift-up placement method onto the electrode array, by using a vacuum transfer method, or by using a stamp transfer method; (c) nanopatteming a dielectric masking layer placed on the TMD surface with an opening which is size-limited so as to allow only a single enzyme biomolecule to attach onto the exposed TMD surface for sequencing analysis; (d) placing the sequencing device into a microfluidic system and supplying a fluid containing denaturized nucleotide molecules or modified nucleotides, and chemical agents; and (e) making an electronic measurement and computer analysis on the event of individual nucleotide monomers or modified nucleotide components attachment onto an enzyme polymerase molecule one at a time to obtain electrical pulse signals to determine the specific nature of the nucleotide being attached.

In some embodiments, the TMD layer is made defective by nanopatteming into linear nano-ribbon parallel array or patterned shape nano-ribbon array, or introducing disturbed lattice defects of strained lattice, vacancies, interstitials, dislocations, chemical doped or ion implant doped regions, or providing nanoporous defects.

In some embodiments, the defects in TMD layer are introduced by beam irradiation selected from ion implantation beam, plasma reactive ion etch (RIE) atmosphere, broadened optical, electron, ion or neutron beam, so as to introduce defect density of at least 10 ⁵ /cm ² .

In some embodiments, the irradiated structure is post-irradiation annealed at 100- 600°C. In some embodiments, the irradiated structure is post-irradiation annealed at less than 100°C. In some embodiments, the irradiated structure is post-irradiation annealed at greater than 600°C.

In some embodiments, the TMD lattice defects or nanopores or nano-pinholes are introduced by chemical etching using oxidizing chemicals, strong acids, strong alkaline solutions, so as to introduce defect density of at least 10 ⁵ /cm ² . In some embodiments, the defect density is greater than 10 ⁵ /cm2, for example, greater than 10 ⁶ /cm ² , greater than

10 7 /cm 2 , greater than 108 /cm 2 , greater than 109 /cm 2 , or greater than 1010 /cm 2.

In some embodiments, the TMD with nanoporous defects are introduced by using block copolymer templated hole generation so as to introduce defect density of at least 10 ⁵ /cm ² . In some embodiments, the defect density is greater than 10 ⁵ /cm2, for example, greater than 10 6 /cm2 , greater than 107 /cm2 , greater than 108 /cm2 , greater than 109 /cm2 , or greater than 10 ¹⁰ /cm ² .

In some embodiments, the TMD with nanoporous defects are introduced by using anodized aluminum oxide templated hole generation so as to introduce defect density of at least 10 ⁵ /cm ² . In some embodiments, the defect density is greater than 10 ⁵ /cm ² , for example, greater than 10 /cm , greater than 10 /cm , greater than 10 /cm , greater than 10 /cm , or greater than 10 ¹⁰ /cm ² .

In some embodiments, the TMD with nanoporous defects are introduced by using nanoimprinting patterning so as to introduce defect density of at least 10 ⁵ /cm ² . In some embodiments, the defect density is greater than 10 ⁵ /cm ² , for example, greater than 10 ⁶ /cm ² , greater than 10 7 /cm 2 , greater than 108 /cm 2 , greater than 109 /cm 2 , or greater than 1010 /cm 2.

In some embodiments, the TMD with nanoporous defects are introduced by using metallic nanoparticles spray deposited onto TMD, allowing diffusional reactions and differential chemical etching.

In some embodiments, the TMD with nano-pinhole defects are introduced by using an incomplete thin film mask deposition so as to prepare a mask with nanoscale pinholes through which the TMD layer underneath can be etched using chemical, plasma or ion bean etching method to create nano-pinhole defects. The mask material is then removed by chemical or plasma etch to expose the TMD layer with nano-pinhole defects of at least 10 ⁵ /cm ² . In some embodiments, the defect density is greater than 10 ⁵ /cm ² , for example, greater than 10 /cm , greater than 10 /cm , greater than 10 /cm , greater than 10 /cm , or greater than 10 ¹⁰ /cm ² .

In some embodiments, the TMD layer material outside a specific region intended for a single biomolecule to be attached is intentionally damaged, with the crystal structure of TMD material affected and behave like an insulator or very high resistivity material with at least 100 ohm-cm, preferably at least 10,000 ohm-cam, even more preferably at least 1 mega ohm- cm resistivity using a processing methods selected from the group consisting of (i) electron beam irradiation, (ii) ion beam irradiation, (iii) optical or laser beam irradiation, (iv) particle beam irradiation, and (v) ion implantation of foreign species atoms.

In some embodiments, the TMD layer material is made to exhibit a hydrophilic state obtained by using one or more of the following processing techniques: (i) by using a plasma treatment using oxygen-containing plasma or other types of plasma containing nitrogen, chlorine, fluorine or mixed elements, or (ii) by using imperfect crystallization with defects such as strained lattice, vacancies, interstitials, dislocations nanopores or aggregated defects) in the M0S2 structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) at lower temperatures during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process temperature selected to be lower by at least 50 °C, preferably by at least 200 °C lower than the temperature for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material, or (iii) by using a non-completed crystallization process with defects such as strained lattice, vacancies, interstitials, dislocations nanopores or aggregated defects) in the M0S2 structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) for shorter time periods during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process time selected to be shorter by a factor of at least 3, preferably by a factor of 10 than the annealing time needed for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material or (iv) by a deposition of a thin hydrophilic surface layer less than 10 nm thickness, such as transition metals like Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Fe, Co, Ni, Cu, Zn, or ceramic islands of these elements such as Ti0 ₂ , NiO, Fe2C>3 using physical deposition, chemical deposition, electrochemical deposition, or ion implantation.

In some embodiments, the TMD layer material is made to exhibit a combined hydrophilic and hydrophilic mixed phase state obtained by using one or more of the following processing techniques; (i) by using a plasma treatment using oxygen-containing plasma or other types of plasma containing nitrogen, chlorine, fluorine or mixed elements, or (ii) by using imperfect crystallization with at least 10%, preferably at least 30% area fraction of TMD surface material having an imperfect crystal lattice configuration, with defects such as vacancies, interstitials, dislocations nanopores or aggregated defects) in the M0S2 structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) at lower temperatures and shorter times during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process temperature selected to be lower by at least 50°C, preferably by at least 200°C lower than the temperature for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material, or (iii) by using a non-completed crystallization process with at least 10%, preferably at least 30% area fraction of TMD surface material having an imperfect crystal lattice configuration, with defects such as vacancies, interstitials, dislocations nanopores or aggregated defects) in the MoS ₂ structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) for shorter time periods during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process time selected to be shorter by a factor of at least 3, preferably by a factor of 10 than the annealing time needed for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material, or (iv) by a partial deposition of hydrophilic islands such as metallic islands of transition metals like Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Fe, Co, Ni, Cu, Zn, or ceramic islands of these elements such as T1O2, NiO, Fe2C>3, with an areal fraction of 5 - 50%, preferably at least 10%, more preferably at least 30%, using physical deposition, chemical deposition, electrochemical deposition, or ion implantation. In some embodiments, the areal fraction is greater than 50%. In some embodiments, the areal fraction is less than 10%.

In some embodiments, the tunable hydrophilic TMD layer material is produced by using the following processing method; (i) a DC or AC electric field is applied to the vertically arranged two electrodes, one above and one below the TMD layer, (ii) with the applied electric field being at least 10 V/nm, preferably at least 30 V/nm to alter the semiconducting properties, (iii) with the bandgap widened by at least 5%, preferably at least 10%, and (iv) with the TMD made more hydrophilic with the water droplet contact angle to decrease by at least 5 degrees, preferably by at least 20 degrees for easier accommodation of fluidic chamber environment and improved adhesion of single enzyme molecule such as DNA or RNA polymerase.

In some embodiments, a method of maintaining the sequencing device is provided of any of the devices described herein, wherein the device when not in use is evacuated and back-filled with inert gas so as to minimize inadvertent adhesion or adsorption of unwanted molecules.

In some embodiments, use of any of the DNA or RNA sequencing devices and systems described herein can perform a whole genome sequencing. In some embodiments, use of any of the DNA or RNA sequencing devices and systems described herein can perform partial genome sequencing.

In some embodiments, use of any of the DNA or RNA sequencing devices and systems disclosed herein can diagnose diseases. In some embodiments, use of any of the DNA or RNA sequencing devices and systems described herein can diagnose diseases such as cancer.

In some embodiments, any of the genome sequences systems described herein can be a desktop unit, a portable unit or a wearable unit. Artificially introduced defects and configurations for enhanced biomolecule attach and improved sensor signal

Referring to the drawing figures, FIGS. 1A-1C schematically illustrate examples of defects that can be artificially introduced to a TMD sheet such as M0S ₂ or WS ₂ , using various techniques to provide an increased bandgap, and/or to provide many active site edge locations for strong adhesion of bridge structures or biomolecules (such as enzyme molecules). The TMD layer can be a single layer type or few layer type. The TMD can be narrow ribbons of linear or zig-zag shape M0S ₂ or WS ₂ 10 as illustrated in FIG. 1A, or can have intentionally damaged surrounding area 12 except for the linear ribbon regions, as illustrated in Fig. IB, or can contain a multiplicity of periodic or random defects 14 as illustrated in FIG. 1C.

With reference to FIG. 1A, linear or zig-zag shape M0S ₂ or WS ₂ ribbon array (single layer of few layer) with nanogaps between ribbons can be obtained by nanopatterned removal of material. The edges of narrow ribbons provide favorable adhesion sites for biomolecules such as an enzyme molecule (e.g., DNA or RNA polymerase). The presence of edge defects also can increase the bandgap for more versatile semiconductor characteristics. In some embodiments, the ribbon width dimension is in the range of 1-500 nm. In some embodiments, the ribbon width dimension is in the range of 3-30 nm. In some embodiments, the gap spacing between the ribbons is in the range of 2-20 nm.

With reference to FIG. IB, the intentionally damaged, insulating or high-resistivity surrounding areas outside the linear or zig-zag shape M0S ₂ or WS ₂ ribbon array regions can be introduced by electron beam radiation, ion beam radiation, or ion implantation, or other optical or particle radiations. In some embodiments, the desired width of the embedded ribbons in FIG. IB is in the range of 1-500 nm. In some embodiments, the desired width range of the embedded ribbon is in the range of 3-30 nm. In some embodiments, the gap spacing between the ribbons is in the range of 2-20 nm.

With reference to FIG 1C, various other types of intentionally induced defects (aside from the ribbon type or areal type defects of FIGS. 1A-1B) are generally illustrated. They can be periodic or random lattice defects (vacancy type or interstitial type, 1-20 nm size regime) artificially introduced larger-than-lattice defects (periodic or random islands, e.g., 2-200 nm size) with circular, square, rectangle or irregular-shape defects [e.g., introduced by lithographic patterning (e.g., e-beam lithography, nano-imprint lithography, template mask induced removal such as using pre-patterned diblock co-polymer membrane, anodized aluminum oxide membrane followed by plasma (or RIE) etch to remove M0S ₂ or WS ₂ type TMD material]. These defects can also be introduced as latent defects by intentionally damaging some the selected areas by e-beam irradiation, ion-beam irradiation, ion implantation, or other optical or particle radiations. Process for nanopatterning of transition metal dichalcogenides layers

Shown in FIGS. 2A and 2B are examples of nanopatterning processes of TMD materials such as M0S ₂ or WS ₂ , using electron beam lithography (FIG. 2A) and nanoimprint lithography (FIG. 2B). In these embodiments, the TMD layer itself is physically reshaped into nanopatterns such as ribbons or islands.

FIG. 2A illustrates the process of e-beam patterning of a M0S ₂ 300 layer using negative or positive resist. The M0S2 300 layer (or a TNS layer in general) is coated with a resist material 302 (e.g., either a well-known positive photoresist layer such as PMMA (poly methyl methacrylate) or a negative photoresist layer such as HSQ (hydrogen silsesquioxane) or SU-8) by spin coating or thin film deposition. The photoresist is then exposed to UV light irradiation (or ion beam, neutron beam or x-ray beam irradiation in terms of general lithography), and a pattern is formed by differential developing and chemical or other process of removal of UV -reacted vs UV-unreacted local regions of the resist layer. A generally higher resolution nanopattern in the resist layer is obtained by using a negative resist than a positive resist. A short time exposure (e.g., shorter than several seconds) to UV, ion beam, neutron beam or x-ray beam irradiation, followed by a colder temperature development of the resist layer (e.g., at or below minus 10°C) generally yields a higher resolution, e.g., sub-10 nm, and desirably sub-5nm resolution. A straight single beam or a multi-beam interference pattern may be utilized for exposure of the resist layer. The nanopatterning can be done into a periodic, non-periodic, or irregular configuration.

Once a resist pattern is obtained, the M0S2 layer underneath is etched through the nanoholes in the resist layer mask by chemical etch or reactive ion etch (RIE) to selectively remove the M0S2 material so as to generate a nano-patterned M0S2, as shown in FIG. 2A. The left-over resist is then chemically etched away to provide a clean, nano-patterned M0S2. FIG. 2B illustrates the process of nanoimprint patterning of an M0S2 layer using a mold to first imprint the resist layer. An alternative method is to intentionally damage the region of TMD outside the needed material area as discussed above by using intentional disruption of crystal structure or lattice structure using e-beam, ion-beam, ion implantation, optical beam, and other radiations. In the nanoimprint processing, a premade, nanosized mold 400 (or a nano-stamp) is prepared first, e.g., by UV, ion beam, neutron beam or x-ray beam irradiation. The nano-stamp is then utilized so as to mechanically impress into the resist layer 402. preferably by pre-heating the resist layer to close to the glass transition temperature where the polymer resist becomes soft for easier mechanical imprinting. The imprint-patterned resist is then subjected to a reactive ion etching (RIE) until the bottom substrate, in this case, the M0S2 layer, is exposed to the chemical or RIE etching to pattern and etch the M0S2 layer. The residual resist layer is then chemically etched away. Molecular bridge sensor construction using size-limited exposed TMD layers for single biomolecule only attachment onto the sensor bridge

Referring to the drawings, FIGS. 3A-3D represent fabrication steps to create an exemplary molecular bridge of DNA or RNA sensor comprising size-limited, M0S2 islands (TMD islands in general). FIG. 3A illustrates the deposit and patterning of conducting electrode pairs 34 (pairs of source and drain electrodes). As illustrated, conducting electrode pairs 35 (Au, Pt, Ag, Pd, Rh, or their alloys, for signal detection), each pair consisting of a source and drain electrode separated by a "nanogap, (e.g., 2-20 nm)" are deposited and patterned on a dielectric substrate 37 such as S1O2 or AI2O ₃ . Then, as illustrated in FIG. 3B, a M0S2 layer 36 (or TMD transition metal dichalcogenide layer in general) is suspended over the nanogap to physically connect source and drain electrodes within each pair of electrodes. This TMD layer may have a regular or narrow-ribbon configuration, or may intentionally be made defective. The TMD layer may be nanopatterned by nanoimprinting or e-beam lithography if needed. FIG. 3C illustrates the step of adding a protective dielectric coating 38 over the M0S2 layer. The dielectric coating is protective and size-limiting, and may be a polymer such as PMMA, or a ceramic layer like S1O2. The dielectric layer 38 size limits the M0S2 layer to exposed areas measuring about 2-20 nm such that a single biomolecule can fit within the limitation and bind to the exposed M0S2 layer (e.g., polymerase enzyme attachment). Lastly, FIG. 3D illustrates allowing, preferably, only a single enzyme molecule 31 (e.g. a DNA or RNA polymerase) to attach onto each exposed size-limited areas of M0S2 36 and bind thereon, to enable each of the nucleotide 35 attachment (nucleotide monomers like A, T, C, G, U, etc.) in the polymerase reaction 33 to change electrical properties of the molecular bridge for sequencing analysis. As illustrated in FIG. 3D, a molecular bridge solid state sensor on a M0S2 island is used for genome or DNA sequencing via detection of a change of current pulse or other signal upon attaching or detaching of a nucleotide 35 or other biomolecule to the single enzyme molecule 3L

In further detail, a conducting electrode pair (e.g., made of highly conductive and corrosion resistant metals such as Au, Pt, Ag, Pd, Rh, or their alloys), (FIG. 3A), is deposited and patterned on the surface of a dielectric substrate like S1O2, AI2O ₃ , or a Si substrate with a relatively thick insulator layer of S1O2, AI2O ₃ , coated on the surface. A nanogap of e.g., 2-20 nm is provided between the two metal lead wires serving as a source and a drain. A suspended TMD like M0S2 layer (regular M0S2 or preferably a M0S2 structure intentionally made defective) is added over the electrode gap as shown in FIG. 3B. One example technique is to get the TMD layer floated on the surface of water or alcohol, and the substrate (with a pre-patterned metal electrode pair) is lifted up from underneath the water or alcohol to collect the TMD layer, followed by a drying procedure.

The TMD sheet is then coated with a protective dielectric coating (e.g., polymer layer like PMMA or ceramic layer like S1O2) and patterned, as illustrated in FIG. 3C, to limit the exposed area of the TMD to nanometer regime island geometry (e.g., 3-30 nm average size). The dimensional limitation allows preferably only a single molecule enzyme 31 (e.g. polymerase) to attach onto the TMD layer, FIG. 3D, preventing a multiple molecule attachment and signal mix-up, and enable each of the enzyme molecules (like DNA or RNA polymerase) to react with a nucleotide 35 to attach onto the polymerase (nucleotide monomers like A, T, C, G, U etc.) to detectably change electrical properties of the molecular bridge for sequencing analysis. The desirable dimension of size-limited exposed TMD layer is preferably less than 30 nm average equivalent diameter, more preferably less than 20 nm equivalent diameter, even more preferably less than 10 nm equivalent diameter, by lithographically defined coverage of dielectric material layer of polymer or ceramic outside a specific region intended for attaching only a single molecule. The size-limited region can have a circular shape, oval shape, square or rectangular shape, or irregular shape, with the equivalent diameter defined here as the calculated diameter of a corresponding equal-area sized circle.

As described and detailed herein, a polymerase is an enzyme that synthesizes long chains or polymers of nucleic acids. For example, DNA polymerase and RNA polymerase can copy a DNA or RNA template strand, respectively, using base-pairing interactions, which is utilized to assemble DNA and RNA molecules. When a particular type of nucleotide or other biomolecule is attached to the enzyme polymerase biomolecule, a unique pulse current signal is generated which provides information on what type of nucleotides is being attached or detached. Part of the sequencing operation includes the nucleotide attachment to form a double-strand DNA associated with the enzyme polymerase.

The biomolecule to be attached on the TMD includes, in addition to various enzyme molecules, various other polymers, DNA, RNA, proteins, ribozyme, aptamer or polysaccharide. Other single molecule functionalizations of these defective TMD structures can provide sensors for other applications besides genome sequencing. For example, an enzyme other than polymerase can be attached, creating a sensor for the activity of that enzyme. This can be used to sense the presence of the enzyme substrate, and can also be used to characterize the precise kinetics of the enzyme, for application to enzyme evolution, selection and optimization. If a single molecule binding probe is attached to the defective TMD, such as a single stranded DNA or RNA oligomer hybridization probe, or an antibody against an antigen, or a protein that engages in a protein-interaction binding, this can be used to sense the binding events, and thus acts as a sensor for the presence of the binding target.

Modified dNTPs for enhanced sequencing applications of bridge molecules

For DNA or genome sequencing applications, the bridge molecule may be conjugated to a polymerase, bound with a primed single-stranded template DNA as shown specifically be element 33 in FIG. 3D, and provided with a buffer containing nucleotides, dNTPs (deoxynucleotide triphosphates) for incorporation. Electric current through the bridge molecule is monitored as dNTPs are incorporated to synthesize the complementary strand of the template DNA. In the preferred embodiment, native dNTPs like A, T, C, G are used (dATP, dTTP, dCTP and dGTP). In another embodiment, any or all of these may be replaced by corresponding modified dNTPs, having various molecular modifications that may enhance the incorporation signals, or produce signals with enhanced differences between the different base (A, C, G, T) incorporation events, for greater accuracy determining the template sequence. Such dNTP modifications could include: modifications of the base, such as 7-deaza forms, 8-bromo forms, or modification of the alpha- and beta- phosphates, such as thiolated forms or bromated forms of these phosphates, or gamma-phosphate modifications, including the addition of phosphates, such as tetra-, penta- or hexa- phosphates forms.

In addition, modifications may include groups added to the terminal phosphate, and it is known that the polymerase is highly tolerant of many diverse groups added to the terminal phosphate, thus providing a large class of modified dNTPs for these purposes. The use of such modified dNTPs to enhance signals does not require any labeling of the template DNA, or any other use of labels; instead, the modified molecular forms modify the conductivity properties of the complex, and thereby directly enhance the resulting electronic detection signals. Throughout this disclosure, whenever the expression "nucleotide" is used, it refers to either the native dNTPs like A, T, C, G (i.e., dATP, dTTP, dCTP and dGTP), or collectively refers to various types of modified dNTPs as described above.

Array structure of size-limited TMD sensor bridges

Shown in FIG. 4 is the top view of an array of TMD bridges like M0S ₂ or WS ₂ bridge molecular sensors, with the TMD positioned as a suspended layer or substrate-adhered layer. FIG. 4 illustrates individual units of molecular bridge sensors comprising a M0S ₂ or WS ₂ layer bridge 49. The exposed island region is surrounded by a patterned defined dielectric coating mask 48 (e.g., PMMA, PDMS, other adhesion-impeding polymer layer or Si02 etc.) to prevent/minimize biomolecule attachment. The molecular bridge sensors comprise conducting electrodes and lead wires 44. The enzyme polymerase 40 molecule is shown only on the lower two electrode pairs. Size-limited (circular, oval, rectangular, square, or other shape) and locally exposed TMD like MoS2 or WS2 46 are shown on the upper two electrode pairs. Massively parallel electronic sequencing analysis can be performed with many devices organized into a system, having as many as 10,000 or even at least 1 million devices. Size- limited (circular, oval, rectangular, square, irregular or other shape ) and locally selectively exposed TMD like M0S ₂ or WS ₂ (preferably defective or porous). A large TMD sheet can be placed by lifting up of floating TMD layer sheet onto device surface covering many pairs of electrodes, and then mask patterned. The exposed island region is surrounded by a pattern- defined dielectric coating mask (e.g., PMMA, PDMS, other adhesion-impeding polymer layer or S1O ₂ etc.) to prevent/minimize biomolecule attachment.

FIGS. 5A-5D illustrate various embodiments of fabrication steps usable to create an exemplary molecular bridge of DNA or RNA sensor comprising size-limited, M0S ₂ islands (TMD islands in general). First, and as shown in FIG. 5A, a conducting electrode pair 54 (source and drain) is deposited and patterned on a substrate, with each source and drain electrode spaced apart by a nanogap. The conducting electrode pair may comprise Au, Pt, Ag, Pd, Rh, or their alloys, for signal detection, and the nanogap may be in the range of about 2- 20 nm. As illustrated in FIG. 5B, a suspended M0S ₂ layer 56A (or transition metal dichalcogenide layer in general), having either a regular structured or defective M0S ₂ , is placed on the electrode pair, suspended across the nanogap. Then, as shown in FIG. 5C, the outer regions of the TND layer 56A like M0S ₂ or WS ₂ is intentionally damaged to convert the layer to the damaged layer 56B. This is accomplished by, for example, doping with ion implantation or by bombardment with electrons or other radiation, converting select regions of the layer to an insulator or to very high resistivity areas so as to serve as an effective mask to enable a single biomolecule (e.g., polymerase enzyme) attachment.

The schematic in FIG 5D describes a single molecule enzyme 51 (polymerase) to attach onto the M0S ₂ molecular bridge solid state sensor on the M0S ₂ island 56A for genome or DNA sequencing via detection of change of current pulse or other signals upon attaching or detaching of nucleotide 55 (nucleotide monomers like A, T, C, G, U etc.) or other biomolecules during sequencing of the double stranded nucleic acid 53.

Suspended configuration vs. substrate-adhered TMD bridge structures for sequencing

Presented in FIGS. 6A-6C are exemplary embodiments of two configurations of

TMD, such as M0S ₂ or WS ₂ , bridge placement. The schematic in FIG. 6A illustrates a suspended TMD bridge 66A while that in FIG. 6B shows a substrate-adhered TMD bridge 66B. A conducting electrode pair 64 comprising a nanogap 67 is positioned on a dielectric substrate 62 (FIG. 6A). A single enzyme molecule 61 (e.g., DNA or RNA polymerase) is attached onto a suspended TMD bridge 66A (FIG. 6A). A nucleotide monomer 65 (A, T, C, G, U, etc.) is detected upon attachment to the double stranded DNA strand 63 (FIG. 6A). A conducting electrode pair is positioned on a dielectric substrate (FIG. 6B). A single enzyme molecule 61 (e.g., DNA or RNA polymerase) is attached onto a substrate-adhered TMD bridge 66B (FIG. 6B). A nucleotide monomer 65 (A, T, C, G, U, etc.) is detected upon attachment to the double stranded DNA strand (FIG. 6B). A M0S ₂ layer (preferably defective or porous) sheet is patterned by e-beam or preferably nano-imprinting lithography and plasma etched, and then is masked by dielectric (e.g., PMMA or adhesion-impeding polymer layer) to prevent biomolecule attachment. A top view of the TMD bridge structure with attached polymerase enzyme is shown in FIG. 6C. The top view shows that the single molecule enzyme (polymerase) on TMD enables each of the polymerase reaction of nucleotide attachment (nucleotide monomers like A, T, C, G, U, etc.) to change electrical properties of the molecular bridge for sequencing analysis. The M0S ₂ sheet 67 (preferably defective or porous) is patterned. The size-limiting of locally exposed M0S ₂ region 69 (circular, square, or other shape), preferably as a defective or porous sheet, for single molecule attachment (e.g., 2-20 nm width), can be accomplished, e.g., by nanoimprint lithography with associated ion plasma etching. This method is preferred over e-beam lithography in order to minimize e- beam damage of the TMD layers.

Use of functionalization for biomolecule bonding

The defective TMD also allows an easy and strong bonding with biomolecules as the TMD edges and defects provide many active sites for atomic bonding and chemical bonding. While a direct adhesion of biomolecules such as enzyme polymerase molecule is more desirable for simpler structuring and less interfacial electrical resistance, embodiments herein not exclude a use of functional bridging to ensure stronger attachment of biomolecules onto TMD. In addition to the direct bonding of the enzyme polymerase biomolecule onto the TMD surface, such a bonding can alternatively be achieved using functionalized ligands.

The enzyme molecule connection to TMD may be via functional groups or ligands. FIGS. 7A and 7B illustrate two exemplary embodiments of a solid state molecular sensor, based on enzyme attachment to a suspended TMD bridge (FIG. 7A) and enzyme attachment to a substrate-adhered TMD bridge (FIG. 7B). The sensors can be used for genome or DNA or RNA sequencing detection via change of current or other signals upon attaching or detaching of nucleotide or other biomolecules. FIG. 7A illustrates a molecular bridge solid state sensor 70 for genome or DNA or RNA sequencing detection via change of current or other signals upon the attachment or detachment of individual nucleotide monomers or other biomolecules. FIG. 7B illustrates an embodiment of a molecular bridge sensor 72 with the TMD layer affixed onto the dielectric substrate via Van der Waals forces and the dielectric coating disposed above it. In some embodiments, a defective or nanoporous TMD layer is used, such as M0S2 or WS2, which is masked to limited size areas (e.g., 2-20 nm each), to enforce only a single molecule attachment per each limited size area, such as by using a patterned dielectric coating (e.g., PMMA, PDMS or other adhesion-impeding polymer layer or S1O2 layer). An enzyme molecule 74 (e.g., DNA or RNA polymerase is linked to a suspended TMD bridge such as M0S2 or WS2 76 (FIG. 7 A) _. Alternatively, an enzyme molecule 74 (e.g. DNA or RNA polymerase) is linked to a substrated-adhered TMD bridge 78 (FIG. 7B). Functionalization paired groups 71 that can be optionally used to link enzyme molecule to TMD include, e.g., streptavidin-biotin pair, antibody-antigen interaction, bifunctional ligands using mercaptocarbonic acids [HS-(CH ₂ )«-COOH, n = 1-15], peptide functional groups, antibody-antigen pair, thiol-alkyne pair, COOH-NH ₂ functional group pair, a thiol-maleimide azide pair, silanization linkage using mercaptosilane compounds, and a NHS (N-hydroxysuccinimide) ester-amine pair. Nucleotide monomers 73 (A, T, C, G, U, etc.) are detected as they are added to the DNA strand. Conducting electrodes and lead wires 75 (Au, Pt, Ag, Pd, Rh, or their alloys, etc.) are used for signal detection. The sensors comprise a dielectric substrate 79 (S1O2, AI2O ₃ , etc.) and a nanogap 77.

FIGS. 8 A and 8B illustrate embodiments of TMD-containing molecular bridge sensors usable for sequencing detection that further comprise a third electrode operating as a gate electrode. Gated structure of TMD bridge sequencing devices may comprise disposition of the gate electrode positioned parallel to the source and drain electrodes 80 (FIG. 8A) or perpendicular to the nanogap spacing 81 between the two (source and drain) electrodes (FIG. 8B). In FIG. 8 A, the gate electrode 82 is facing the device junction in a parallel geometry for triode type sensor operation. In FIG. 8B, the gate electrode 83 is facing the device junction in a perpendicular way for triode type sensor operation. The TMD or M0S2 or WS2 (defective or porous TMD) sheet is masked by a dielectric surrounding 84 to prevent biomolecule attachment. The dielectric masks TMD except in a selected limited area. The conducting electrodes (source & drain) contain a nanogap (e.g., 2-50 nm). The tip of the gate electrode can also be placed above or below the nanogap. In either embodiment illustrated, the TMD bridge may comprise M0S2 or WS2.

Intentionally damaged surrounding TMD region

FIG. 9 illustrates a top view of an array of TMD bridge molecular sensors like M0S2 or WS2 with the TMD layer positioned as a suspended layer or substrate-adhered layer. The enzyme polymerase molecule 90 is shown only on the lowest molecular bridge sensor 99. comprising a M0S ₂ layer bridge. FIG. 9 comprises units of molecular bridge sensors comprising a M0S ₂ layer bridge 99. Each molecular sensor comprises conducting electrodes and lead wires 91. As illustrated in FIG. 9, intentionally damaged surrounding TMD region 98, such as M0S ₂ or WS ₂ , may be processed by doping with ion implantation or by bombardment with electrons or other radiation, to be converted to an insulator or very high resistivity region so as to serve as an effective mask. Circular or rectangular or other shaped regions 96 of undamaged M0S ₂ (preferably defective or porous) having the exposed island region 92 surrounded by damaged M0S ₂ having insulative properties or very high resistivity. Optional addition of dielectric mask material, (e.g. PMMA, PDMS, other adhesion-impeding polymer layer, or S1O ₂ and other oxide or nitride dielectric layer) is not excluded from the scope of the embodiments disclosed herein. A multiple array of conducting electrode and lead wires 91 (e.g. Au, Pt, Ag, Pd, Rh, or their allows, etc.) may be used for signal detection. Massively parallel electronic sequencing analysis can be performed with many devices organized into a system, having as many as 10,000 or even at least 1 million devices. Intentionally damaged surrounding TMD region 98 (such as constructed with M0S ₂ or WS ₂ ) can be utilized, e.g., with a processing such as by doping with ion implantation or by bombardment with electrons, ion beams or other optical or particle radiations), to be converted to an insulator or very high resistivity region so as to serve as an effective mask. The high resistivity region is made to have a resistivity value of at least 100 ohm-cm resistivity, preferably at least 0.1 mega ohm-cm resistivity for the regions outside a specific region intended for attaching only a single molecule. Circular or rectangular geometry central region of undamaged M0S ₂ (preferably defective or porous), with the exposed island region surrounded by damaged M0S ₂ having insulator or very high resistivity characteristics can be constructed. While dielectric polymer or insulating silica masking may not be needed in such an intentionally severely damaged TMD mask surrounding the core undamaged or less-damaged TMD region, thus providing a reduced probability of electrical signal interference and reduced chance of biomolecule attachment, an optional addition of dielectric mask material, e.g., PMMA, PDMS, other adhesion-impeding polymer layer, or S1O ₂ and other oxide or nitride dielectric layer) is not excluded as these additional dielectric mask will help to prevent biomolecule attachment. Hydrophilic-hydrophobic composite structured bridge surface

Surface wettability is an important aspect for handling of biomolecules and related components including DNAs, RNAs, nucleotides, enzymes, polymerase and so forth in aqueous environment such as in microfluidic devices for label-free genome sequencing systems. High-quality and clean TMD layers are in general hydrophobic. In some embodiments, the surface of the TMD layer is at least partially converted to a hydrophilic or super-hydrophilic surface. The hydrophilic surface is arbitrarily defined here as a surface with a water droplet contact angle of at most 50 degrees, preferably at most 30 degrees, even more preferably at most 15 degrees.

As illustrated in FIGS. 10A-10B, the TMD molecular bridge structure comprising electrode pairs 206. can be made to have a wholly hydrophilic surface 200 (FIG. 10A) or partly hydrophilic surface 202 (FIG. 10B) to enhance biomolecule attachment, e.g., by using plasma treatment using oxygen-containing plasma (or other types of plasma containing nitrogen, chlorine, fluorine or mixed elements), or using imperfect crystallization (by at least 10%, preferably at least 30% area fraction of TMD surface material having an imperfect crystal lattice configuration, with defects such as vacancies, interstitials, dislocations or aggregated defects) of M0S ₂ type structure, e.g., by sulfurization/annealing at low temperature (or TMD structure in general). The TMD sheet 204 (e.g., preferably defective or porous like MoS2 or WS2) sheet, masked by dielectric (e.g., PMMA or adhesion-impeding polymer layer) to prevent biomolecule attachment.

An example of imperfect crystallization is to intentionally perform a less complete sulfurization annealing (or selenium or tellurium diffusion anneal process) at lower temperatures and shorter times. The annealing temperature after diffusional alloying of sulfur, selenium or tellurium into a deposited metal layer of transition metals (such as Mo, W, Zr, Hf, Co, Ni) is selected to be at least 50° C, preferably at least 200° C lower than the temperature so that less completely crystallized structure with defects can be obtained as compared with the case of higher temperature anneal for obtaining a high-quality crystallization with more than 90% of the material having well crystallized TMD layer material.

Alternatively, a non-completed crystallization process can be applied with at least

10%, preferably at least 30% area fraction of TMD surface material having an imperfect crystal lattice configuration, with defects such as vacancies, interstitials, dislocations nanopores or aggregated defects) in the M0S ₂ structure (or TMD structure in general), e.g., by sulfurization anneal (or selenium or tellurium diffusion anneal process) for shorter time periods during sulfurization synthesis of TMD layer from the pre-deposited metal layer, with the process time selected to be shorter by a factor of at least 3, preferably by a factor of 10 than the annealing time needed for obtaining high-quality crystallization with more than 90% of the material having well crystallized TMD layer material.

Exemplary embodiments illustrating two configurations of hydrophilic-enabled TMS bridge surface structures are presented in FIG. 10A and FIG. 10B. The structure in FIG. 10A represents wholly hydrophilic bridge surface 200. The hydrophilic region is patterned or synthesized as a less perfect crystals (e.g., -3-20 um width). Another embodiment,, is to introduce a composite (i.e. hydrophilic and hydrophobic) mixed surface configuration as described in FIG. 10B, which illustrates a composite configuration mix of hydrophilic islands and hydrophobic regions matrix regions 202. Such a composite hydrophilic-hydrophobic configuration enables easier biomolecule attachment and also allows other local covalent or hydrophobic-hydrophobic bonding to be utilized. The size of either hydrophilic islands or hydrophobic islands is desirably 1-30 nm, preferably 1-10 nm, more preferably 1-5 nm, with the area fraction in the 85-15 ratio (or 15-85 ratio), preferably 70-30 ratio (or 30-70 ratio), even more preferably 50-50 ratio. The hydrophilic portion can be made by using masked plasma treatment (e.g., exposure to oxygen plasma), or by employing defective TMD layer (e.g., incomplete crystallization), or a partial deposition of hydrophilic islands such as metallic nanoislands of transition metals like Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Fe, Co, Ni, Cu, Zn, or ceramic nanoislands of these elements such as T1O2, NiO, Fe2C>3., with an a real fraction of 5 - 50%, preferably at least 10%, more preferably at least 30%, using physical deposition, chemical deposition, electrochemical deposition, or ion implantation, with an a real fraction of 5 - 100%, preferably 10 - 50%.

Such a composite hydrophilic-hydrophobic configuration, enables improved biomolecule attachment frequency with the adhesion improvement by at least 30%, preferably by at least 50%, even more preferably by at least 100% increased adhesion event as compared to the all hydrophobic TMD surface during microfluidic chamber processing of fluid supplying to provide biomolecules, nucleotides, and related biological or chemical components, as well as washing or fluid replacement operations. The size of either hydrophilic islands or hydrophobic islands is desirably 1-30 nm, preferably 1-10 nm, and more preferably 1-5 nm. In either embodiment of FIG 10A and 10B, the TMD (e.g., preferably defective or porous like M0S2 or WS2) sheet, is masked by a dielectric 204 (e.g., PMMA or adhesion-impeding polymer layer) to prevent biomolecule attachment. Conducting electrodes and lead wires 206 (Au, Pt, Ag, Pd, Rh, or their alloys, etc.) are used for signal detection. Size-limited, locally exposed TMD region (circular, square, or other shape) allows for single molecule attachment (e.g., 2-20 nm).

Use of tunable electric field to alter hydrophilicity/hydrophobicity and bandgap property

Shown in FIG. 11 is a cross-sectional view of hydrophilicity-controllable TMD bridge molecular sensors based on TMD layers like M0S ₂ or WS ₂ with the TMD positioned as a suspended layer (or substrate-adhered layer). The suspended TMD bridge is attached and fixed onto the substrate by van der Waals force and a size-limited bridge using dielectric mask coating. The molecular bridge solid state sensor performs genome or DNA sequencing detection via change of current or other signal specifics upon attaching or detaching of a series of nucleotides or other biomolecules to the enzyme polymerase.

In some embodiments, vertical electrodes are positioned below and above the sensor bridge structure as in FIG. 11 to apply an electric field to alter the semiconducting properties (to widen the bandgap) and make the TMD more hydrophilic for easier accommodation of fluidic chamber environment and improved adhesion of single enzyme molecule such as DNA or RNA polymerase. The desired intensity of the vertical electric field to be applied is at least 10 V/nm, preferably at least 30 V/nm, in order to convert the TMD layer from hydrophobic to hydrophilic for enhanced biomolecule attachment, then the field is removed to return to a hydrophobic surface to avoid unnecessary attachment of biomolecules.

FIG. 11 illustrates an additional embodiment of a molecular bridge solid state sensor 114 that can be used genome or DNA sequencing detection via a change or current or other signals upon attaching or detaching of nucleotides or other biomolecules to polymerase. As illustrated in FIG. 11, a suspended TMD bridged 110 that is attached/affixed by van der Waals forces and dielectric mask coating. A single enzyme biomolecule 112 is attached onto the size limited TMD bridge 110. A vertical electrical field 111 (>10 V/nm, preferably >30 V/nm) is applied to convert the TMD layer from hydrophobic to hydrophilic for biomolecule 112 attachment. The electric field is then removed so that the surface is converted back to a hydrophobic surface to avoid unnecessary attachment of biomolecules, or to more easily remove the previously attached biomolecules as needed. After biomolecule e.g., DNA or RNA polymerase) attachment, the addition of a nucleotide monomer 113 (A, T, C, G, U, etc.) is be detected upon a change in the electrical signal after attachment of the monomer to the DNA strand.

Such a tunable electric field also serves another important function, i.e., to more easily remove the previously attached biomolecules via hydrophilicity/hydrophobicity alterations as needed, so that a new fresh biomolecule such as a single enzyme polymerase molecule like DNA or RNA polymerase can now be attached onto the size-limited TMD bridge location in order to continue genome sequencing indefinitely without having to replace the bridge or the sensor assembly. An application of DC electric field or AC electric field can be utilized for enhanced attachment or detachment of the biomolecule.

An array of these DNA or genome sequencing sensors can be made as a massively parallel sequencer system, having as many as 10,000 or even at least 1 million devices.

Split, nanogapped TMD as a well-adherable substrate for tunnel junction construction

Shown in FIG. 12 is a molecular bridge solid state sensor 120 using nanogapped TMD for genome or DNA sequencing detection. As shown in FIG. 12 a split, nanogapped TMD island regions like MoS2 or WS2 121 and a well-adhereable substrate for tunnel junction is used. The TMD island is split into two regions with a nanogap 122 of 2-20 nm between the two TMD regions. When a nucleotide 123 or other biomolecule is attached to the enzyme biomolecule 125 (e.g., DNA or RNA polymerase) in the M0S ₂ type TMD nanogap 122 in a tunnel junction configuration, a unique pulse current signal is generated at the split-TMD tunnel junction, which provides information on what type of nucleotide is being attached. Conducting electrode pairs and lead wires 124 (Au, Pt, Ag, Pd, Rh, or their alloys, etc.) are used for signal detection. The drawing of FIG. 12 shows a side view of the molecular bridge solid state sensor using nanogapped TMD for genome or DNA sequencing detection. Changes of current pulse shape and intensity, or other signal aspects, are measured upon the attaching or detaching of a nucleotide or other biomolecule at the split-TMD tunnel junction configuration.

Block copolymer membrane based alteration of TMD structure for intentional defects

The TMD layer can be processed using nanotemplating to induce a very high density of nanopore type defects, which can increase bandgap as well as enhance the adhesion of the biomolecule (e.g., enzyme molecule of DNA or RNA polymerase) onto the TMD surface for robust and reliable sequencing. Shown in FIGS. 13A-13F is an exemplary fabrication procedure using diblock copolymer mask to produce a nanopatterned TMD bridge. A TMD layer 130 can be grown by various known methods such as CVD synthesis, exfoliation or sulfurization activation of thin deposited metal layer surface. The drawing of FIG. 13A shows the resulting TMD layer like M0S ₂ or WS ₂ on a metal foil, forming the starting material. Synthesis of the TMD like M0S ₂ or WS ₂ layers can occur through exfoliation, CVD, or sulfurization of metal film. After the metal is etched away (FIG. 13B), the floating TMD layer 131 in water or solvent 132 is transferred by lifting up onto the device surface, e.g., nano-gapped, Au, Pd or Pt electrode pair on S1O ₂ (or SiC -coated Si substrate) 133. to position the TMD layer as a suspended bridge.

The TMD surface on top of the device above the M0S ₂ layer 131 and substrate layer

133 is then covered by a thin layer of evaporated SiO? 134 and a lift-up-deposited or transfer- deposited thin film of spin-coated block-copolymer, e.g., PS-b-P4VP copolymer 135. as shown in FIG. 13C. The PS-b-P4VP type block-copolymer film is annealed and RIE is used to remove one of the phases. This results in a nanoscale two-phase structure, leaving the porous PS matrix 136 as the template for subsequent patterning (as shown in FIG. 13D) on which a fluoride-based reactive ion etching (RIE) is performed to remove the M0S ₂ layer. The Si02 oxide layer is penetrated and patterned, partially degrading the PS film, and forming the hard mask hole pattern out of the thin S1O ₂ 137. as shown in FIG. 13E. The TMD layer in the exposed hole area is etched away by O ₂ plasma that penetrates through the hole array in the silica mask layer, after which the S1O ₂ mask is removed by etching. Finally, nanoporous TMD on S1O2 substrate is obtained 138. as shown in FIG. 13F which is then patterned into a size-limited island TMD by dielectric masking to allow only a single molecule attachment (e.g., an enzyme polymerase biomolecule) for nucleotide attachment analysis.

An alternative method of placing the TMD layer on the substrate is to utilize a transfer method (instead of lift-up method using a floating TMD membrane from a solution), e.g., using a gentle vacuum device or a stamp to pick up the TMD sheet and release it on the desired location on the substrate surface, optionally using a releasing agent material at the interface between the pick-up device and the TMD layer.

Various types of diblock copolymers or triblock copolymers can decompose into different types and sizes of two phase structures, and the block copolymer masked patterning approach can produce desirably -2 - 50 nm size defects, preferably 2 - 10 nm size defects on TMD for bandgap opening and enhanced biomolecule adhesion. The desired density of artificially introduced nanopores on TMD by block copolymer template approach is at least

5 2 7 2 10 2

10 /cm preferably at least 10 /cm , even more preferably at least 10 /cm .

AAO membrane based alteration of TMD structure for intentional defects

Other templates other than diblock copolymers can also be utilized for nanoporous

TMD synthesis, e.g., AAO (anodized aluminum oxide) membrane. Shown in FIGs. 13G-13L is an AAO membrane based nanopatterning of TMD for molecular bridge sensors useful DNA sequencing. The TMD layer 140 synthesized by CVD, exfoliated, or made by diffusional synthesis of S, Se, Te onto thin metal surface, FIG. 13G, is placed on a substrate 141 by list-up process, shown in FIG. 13H. An alternative method of placing the TMD layer on the substrate, prior to placement of AAO membrane is to utilize a transfer method (instead of lift-up method using a floating TMD membrane from a solution), e.g., using a gentle vacuum device or a stamp to pick up the TMD sheet and release on the desired location on the substrate surface, optionally using a releasing agent material at the interface between the pick-up device and the TMD layer.

The AAO nanohole membrane 142 fabricated (FIG. 131) is placed on TMD (M ₀ S ² ) e- coated substrate surface 143 (FIG. 13 J) followed by RIE etching of TMD through the AAO array holes 144 (FIG. 13K) and removal of AAO template to obtain nanoporous TMD layer to reveal the nanopatterned M0S2 layer 145 (FIG. 13L). The desired density of artificially introduced nanopores on TMD by AAO template approach is at least 10 ⁵ /cm ² preferably at least 10 ⁷ /cm ² , even more preferably at least 10 ¹⁰ /cm ² . FIG. 13M is an image of exemplary patterning of M0S2 layer using AAO membrane to produce an 80 nm diameter hole array. The floating AAO membrane of FIG. 13G was collected onto the top surface of M0S2 layer coated S1O2 substrate, and the nanopatterning was conducted using BC¾/Ar plasma etching at 100 W under 4.5 mTorr for 4 min, with the AAO as the mask.

FIG. 13G shows TMD synthesis like MoS ₂ or WS ₂ through exfoliation, CVD or sulfurization on metal foil. After the metal is etched away, the M0S2 layer is floating in water or solvent 146 (FIG. 13H). The floating M0S2 147 layer is transferred by lifting it up into the device surface on S1O2 (or Si02-coated Si substrate), to position the TMD layer as a suspended bridge (FIG. 13H). An AAO nanohole membrane 142 is synthesized (e.g., by anodization of AI foil) and the AI matrix is dissolved away (FIG. 131). The AAO membrane is floated in solvent or water 148 and the M0S2 coated substrate 143 is lifted up to pick up the AAO membrane 149 (FIG. 13 J). A layer of dry AAO coating is added and RIE is performed to penetrate the AAO masked holes 144 (FIG. 13K). The AAO is removed to produce nanopatterned TMD like M0S2 or WS2, 145 (FIG. 13L). The nanopatteming was conducted using BC¾/Ar plasma etching at 100 W under 4.5 mTorr for 4 min, with the AAO used as the mask.

Defective TMD layers obtained by nanopore generation, such as via the processes described, for example, in FIGS. 13A-13M, may be additionally and optionally post-etch annealed (e.g., at 100°-600° C for 10 minutes to 24 hrs.) for bandgap change and easier biomolecule attach.

Yet another embodiment to generate nanoporous TMD is to utilize nanoimprinting patterning (see, for example: FIGS. 2A-2B) so as to introduce a defect density of at least 10 ⁵ /cm ² . A master nanoimprinting mold (e.g. stamps), such as, with 10 nm regime nanoislands, nanoholes or nanolines, can be generated by e-beam lithography. Many daughter stamps can then be generated using the known pattern transfer techniques to allow nanopatteming of many devices.

Evolution or mask layer being deposited on graphene

At the early stage of deposition, the mask material can have more defective structure like Fig. 14A or B. As the film gets thicker for longer period deposition (e.g., by sputtering or evaporation), the pinholes or defects gradually become less frequent as shown in Fig. 14C and D. FIG. 14A shows graphene 162 on a support 164 (sequencing structure base or split substrates for graphene suspension). Atoms 160 are being sputtered on the surface of graphene 162. Plasma etch 166 is carried out to create graphene with nanodefects 168 (FIG. 14E). Defective or nanoporous TMD layer by diffusional reaction with metallic nanoparticles

Desirably defective TMD or nanoporous TMD can also be prepared by thermally induced reaction of TMD material with metallic nanoparticles. Shown in FIGS. 15A-15D is an exemplary defective or perforated TMD like M0S2 or WS2 for molecular bridge sensors for DNA, RNA or genome sequencing. As shown in FIG. 15 A, the surface of the TMD layer 150 is coated with metallic nanoparticles (NPs with 1-20 nm dimension), e.g., by early stage of island type thin film deposition of e.g., Cu, Zn, In, Sn, Al, by sputtering or evaporation, which is optionally followed by annealing to ball up the metal into nanoparticles 151 (nanoislands) (as shown in FIG. 15B), which upon further annealing will form compositionally altered island array 152 through diffusional reactions to form altered composition defects, or nanopores in the TMD layer by differential chemical etching or RIE etching (as shown in FIG. 15C). The altered TMD nanoregions become defective by reaction with 1-20 nm size nanoparticles (e.g., local TMD diffusional composition change with metallic nanoislands). These nanoislands can also be differentially chemical or RIE etched way for creation of nanopores in the TMD layer, which could allow for easier biomolecule attachment and for additional bandgap opening, if desired. Electrical lead wires 153 and size- limiting dielectric layer 154 (polymer or ceramic) is then added (as shown in FIG. 15D) to make the solid state electronic sensor for single enzyme molecule attachment and associated analytes attachment and sequencing analysis. The electrical lead wires 153 (Au, Pt, Pd, alloys) detect a nucleotide monomer 155 (A, T, C, G, U, etc.) upon attachment of the monomer to a strand of DNA (as shown in FIG. 15D). A single enzyme molecule 156 (e.g., DNA or RNA polymerase) is attached onto a size-limited TMD bridge (as shown in FIG. 15D).

FIGS. 15A-15D also illustrate a method of manufacturing molecular bridge DNA or

RNA sensors comprising perforated and/or defective TMD such as M0S2 or WS2. FIG. 15A shows a TMD layer 150 deposited on a dielectric substrates 157. as obtainable by any of the methods described above. FIG. 15B shows coating the TMD surface with 1-20 nm sized metallic nanoislands 151. As mentioned, this step may comprise early stage island-like thin film deposition, optionally followed by annealing to ball up the metal into nanoislands. FIG. 15C demonstrates inducing diffusional reactions by heating to form altered composition defects or nanopores in the TMD layer, such as by differential chemical etching or RIE etching. FIG. 15D shows adding electrical lead wires 153 and a size-limiting dielectric layer 154 (e.g. polymer or ceramic). Each size-limited region is then disposed to accept a single enzyme molecule for attachment to the exposed TMD. The final sensor resulting thereby is a solid state electronic sensor for analyte attachment and sequencing analysis.

The desired density of artificially introduced nanopores on TMD is at least 10 ⁵ /cm ² preferably at least 10 ⁷ /cm ² , even more preferably at least 10 ¹⁰ /cm ² . On such nanoporous TMD, electrical lead wires and size-limiting dielectric layer (polymer or ceramic) can be added to make the solid state electronic sensor for single enzyme molecule and associated analytes attachment and sequencing analysis. The single molecule enzyme (polymerase) on TMD enables each of the polymerase reaction of nucleotide attachment (nucleotide monomers like A, T, C, G, U or modified nucleotides) to uniquely change electrical properties of the molecular bridge for DNA, RNA or genome sequencing analysis.

Instead of using a phase decomposition, a porous mask, nanoparticles and other approaches, a defective TMD can also be obtained by a beam irradiation for enhanced molecular bridge DNA or RNA sensors. As shown in FIGS. 16A-16D, a TMD layer disposed on the electrode system can be irradiated by ion implantation beam, plasma reactive ion etch (RIE) atmosphere, broadened optical, electron, particular or neutron beam. The defective TMD layer so obtained by irradiation (with an optional addition of post-irradiation annealing), can be combined with electrical lead wires and size-limiting dielectric mask layer (polymer or ceramic) to make the solid state electronic sensor for single enzyme molecule and associated analytes attachment and sequencing analysis. The desired density of defects in TMD produced by irradiation is at least 10 ⁵ /cm ² , preferably at least 10 ⁷ /cm ² even more preferably at least 10 ¹⁰ /cm ² . DNA, RNA or genome sequencing analysis is enabled when the single molecule enzyme (polymerase) on TMD causes each of the polymerase reactions of nucleotide attachment (nucleotide monomers like A, T, C, G, U or modified nucleotides) to uniquely change electrical properties of the molecular bridge sensor.

Such defective TMD layers obtained by beam irradiation may be additionally post- etch annealed (e.g., at 100-600 °C for 10 minutes to 24 hrs. for stress relief treatments or atomic rearrangements) for bandgap change and easier biomolecule attachment, as exemplified in FIGS. 16A-16D.

The method illustrated in FIGS. 16A-16D begins with placement of a TMD layer 160 on a dielectric substrate 161 (S1O2, AI2O ₃ , etc.) (as shown in FIG. 16A). FIG. 16B illustrates the TMD being broad-beam irradiated with ion implantation beam (e.g., with N, C, F, O, H, Ar, Ni, Ti, Mn, Fe, Cu, AI, and other species), plasma reactive ion etch (RIE) atmosphere, broadened optical, laser beam, electron, ion or defocused neutron beam 162. The broad beam irradiation with ion implantation may include any of N, C, F, O, H, Ar, Ni, Ti, Mn, Fe, Cu, or Al, or other species, and the broad beam may include plasma RIE defocused neutron beam, laser beam and/or electron beam. In FIG. 16C, defective TMD is produced by irradiation 163. Optional post-irradiation annealing may be used to induce point defects, interstitials or agglomerated nanoparticles or nanopore defects for bandgap change and for easier biomolecule attachment. In FIG. 16D, electrical leads 164 (Au, Pt, Pd, alloys) are added along with the size-limiting dielectric mask layer 165 (polymer or ceramic) for single molecule attachment, creating a solid state electronic sensor for detection and analysis of analyte attachment and sequencing. Nucleotide monomers 166 (A, T, C, G, U, etc.) are detected by the electrical lead wires upon attachment to the DNA strand. A single enzyme molecule 167 (e.g., DNA or RNA polymerase) is attached onto a size-limited M0S ₂ bridge. The density of defects in the TMD layer like M0S ² and Ws ² is at least 10 ⁵ /cm ² , preferably at least 10 ⁷ /cm ² .

Nanoscale or lattice-scale defects can also be created, by using various chemical reactions. FIGS. 17A-17D illustrate an embodiment of a method for manufacturing a chemically induced defective TMD layer like M0S ₂ or WS ₂ . (with disturbed lattice regions or nanopores). As shown in FIGS. 17A-17D, a TMD layer 170 (as shown in FIG. 17A) is chemically etched on the TMD surface in an electrochemical etching bath 172 (as shown in FIG. 17B), which creates defective TMD 171 (with the optional addition of post-etch annealing) (as shown in FIG. 17C). Electrical lead wires 173 and a size-limiting dielectric layer 174 (polymer or ceramic) are used to make the solid state molecular electronic sensor for single enzyme molecule and associated analytes attachment and sequencing analysis (FIG. 17D). The TMD layer 170 is on a sequencing solid state sensor substrate 175 (dielectric substrate (S1O ₂ , AI ₂ O ₃ , etc)) (FIG. 17A) and is immersed in a chemical etching or electrochemical etching bath 172 (FIG. 17B). The steps in chemical etching may comprise an oxidizing reaction etch, with (i) acidic solutions including concentrated H ₂ SO ₄ , HNO ₃ , KCIO ₃ , or their mixtures, preferably hot, (ii) alkaline solutions like hot KOH or NaOH, or (iii) use of a de-alloyed and nanoporous layer of Au-Ag alloy as a mask to etch the TMD surface. Chemical etching creates a defective TMD layer 171 (FIG. 17C). The chemically modified TMD may optionally be given a post-irradiation annealing (e.g., 100-600° C for 10 minute to 24 hrs.) to optimize the defective structure for enhanced bandgap change and easier biomolecule attach. Electrical lead wires 173 and a size-limiting dielectric layer 174 (polymer or ceramic) are then added (FIG. 17D) to make the solid state electronic sensor for single enzyme molecule and associated analytes attachment (e.g., nucleotide monomer (A, T, C, G, U, or modified nucleotides) and sequencing analysis.

Chemical etching can be performed, e.g., as an oxidizing reaction etch, with i) acidic solutions including concentrated H ₂ SO ₄ , HNO ₃ , KCIO ₃ or their mixtures, preferably using a hot solution, or ii) alkaline solutions like hot KOH or NaOH, or iii) by using a de-alloyed and nanoporous layer of e.g., Au-Ag alloy film (2-20 nm thickness, sputter or evaporation deposited) as a mask to etch the TMD. Defective TMD obtained by chemical etching, such as for example by the method illustrated in FIGS. 17A-17D, may be optionally and additionally post-etch annealed (e.g., at 100-600° C for 10 minutes to 24 hrs.) for stress relief annealing, bandgap change, and easier biomolecule attachment.

Three-dimensionallv shaped TMD layer for sequencing by shape-altering of 2D configured TMD

While the TMD layers employed are typically have been described mostly as a flat layer above, embodiments herein also encompasses a non-flat, three-dimensional (3D) shaped TMD layers as another possible embodiment. Shown in FIGS. 18A-18D illustrate an example of altering a 2D layer to a 3D configuration so as to induce new modes of defects and shape discontinuity for higher-energy-state local regions. FIGS. 18A-18D illustrate a shape-altered TMD layer induced by a dielectric insert in or near the nanogap. Such an insert serves to provide additional defects for enhanced biomolecule adhesion. The insert can be left permanently underneath the TMD layer as a mechanical support, or can be dissolved away. In the FIG. 18A suspended MoS ₂ or WS ₂ layer 1808 (or TMD transition metal dichalcogenide layer in general), having a regular, or narrow-ribbon configuration (or a TMD layer intentionally made defective by processing) is nanopatterned by nanoimprinting (preferably) or e-beam lithography if needed. Conducting electrode pair 1804 is selected from a film of a patterned stable metal such as Au, Pt, Ag, Pd, Rh, or their alloys for signal detection) with a nanogap between each pair typically being in the range of e.g., 2-20 nm (FIG. 18A).

A shape-altered TMD layer 1806B is produced by inserting a shape-altering dielectric insert 1807 in the nanogap 1810. to provide additional defects for enhanced biomolecule adhesion. The shape-altering insert results in a shape-altered TMD layer as depicted in 1806B. 1086C, and 1086D. The shape-altering insert can be added by physical or chemical or solution deposition and back etch, deposition and patterning via lithography, or gap filling and solidification. Such a shape-altering insert may comprise a dielectric material selected from polymer materials such as PMMA ((poly)methylmethacrylate), HSQ (hydrogen silsesquioxine), or ceramic materials like S1O2, AI2O ₃ , MgO and other dielectric materials. The shaped inserts can be left under the TMD layer for mechanical reinforcement, such as in FIG. 18B, or optionally removed if desired as illustrated in FIG. 18C or FIG. 18D. The desired shape-altering insert structure can be made and deposited at the nanogap between the two electrodes, e.g., by physical or chemical or solution deposition and optional back etch, deposition and patterning via lithography, or gap filling and solidification. The shape- altering insert structure can also be deposited or placed, not just in the nanogap, but on the top surface of the electrode, if desired, For example, the TMD layer can be deposited on top of the size-limited 2-20 nm diameter metallic islands of Au, Pt, Ag, Pd, Rh, or their alloys, which are sometimes utilized to attach a single polymerase enzyme molecule onto the electrode pair.

Shape-altered TMD layer (such as M0S2, WS2) can optionally have a nanoporous structure, irradiated structure, lattice-defective structure with vacancies, aggregates of pores or interstitials, chemically etched defects, ion implanted defects, and so forth. The shape- altering inserts can be left as is or removed by solvent, acid or reactive ion etching (RIE). The altered shape can be hemispherical, rectangle, oval, wavy or other periodic or irregular geometry. The insert can also have some sharp or jagged tips so as to intentionally cause a local puncturing or tearing of TMD. These intentionally altered shapes provide additional defects at the curved or kinked position with displaced or strained lattice in TMD, which locally changes bandgap, and produces higher energy state positions for enhanced adhesion of enzyme biomolecules. The result of using a shape-altering insert structure 1807 is a shape- altered TMD layer, such as 1806b. 1806c. or 1806d, optionally having nanoporous structure, irradiated structure, defective structure with lattice vacancies, aggregates of pores or interstitials, chemically etched defects, ion implanted defects, or the like. The shape-altering inserts 1807 may be left in as mentioned, or removed by solvent, acid, or PJE. The altered shape may be hemispherical, rectangular, oval, wavy, or any other periodic or irregular geometry. Further, the altered shape may be any shape such that the TMD is punctured or torn. These altered shapes provide additional defects at the curved or kinked position comprising displaced or strained lattice in the TMD, which locally changes bandgap and produces higher energy state positions for enhanced adhesion or enzyme biomolecules. The desired shape-altering insert structure can be made and deposited at the nanogap between the two electrode, e.g., by physical or chemical or solution deposition and optional back etch, deposition and patterning via lithography, or gap filling and solidification. The shape- altering insert structure can also be deposited or placed, not just in the nanogap, but on the top surface of the electrode, if desired. For example, the TMD layer can be deposited on top of the size-limited, 2-20 nm diameter metallic islands of Au, Pt, Ag, Pd, Rh, or their alloys, which are sometimes utilized to attach a single polymerase enzyme molecule onto the electrode pair.

Shape-altered TMD layers (such as M0S2, WS2) can optionally have a nanoporous structure, irradiated structure, lattice-defective structure with vacancies, aggregates of pores or interstitials, chemically etched defects, ion implanted defects, and so forth. The shape- altering inserts can be left as is or removed by solvent, acid or reactive ion etching (RIE). The altered shape can be hemispherical, rectangle, oval, wavy, or other periodic or irregular geometry. The insert can also have some sharp or jagged tips so as to intentionally cause a local puncturing or tearing of TMD. These intentionally altered shapes provide additional defects at the curved or kinked position with displaced or strained lattice in TMD, which locally changes bandgap, and produces higher-energy-state positions for enhanced adhesion of enzyme biomolecules.

As illustrated in FIG. 18B, the insert can be left permanently underneath the TMD layer to serve as a beneficial mechanical support (e.g., to guard against mechanical detachment or damage of the TMD layer during microfluidic handling of the sequencing device systems and associated inadvertent force applied to the suspended or barely bonded TMD layer on the nanogap region). Thus such an intentionally added protruding insert structure in the nanogap serve a dual function of (i) mechanical reinforcement for enhanced durability /reliability of the attached TMD layer during a microfluidic operation or washing (and associated durability of the linked polymerase biomolecule and single/double strand DNAs on TMD near the nanogap), and (ii) enhancement of attachment of polymerase type enzyme biomolecule (or any desired biomolecule in general) onto the nanogap for sequencing operations.

Solid state molecular sensors for nucleic acid sequencing device comprising a combined structure of size-limited TMD and a single biomolecule enzyme polymerase, such as any of the embodiments illustrated in FIG. lA-FIG. 18D can be made into an array of at least thousands of device assembly, as illustrated in FIG. 19. The availability of many parallel devices makes the sequencing analysis to be conducted faster, with more accuracy. Also, such a parallel processing scheme will make the overall system less costly. FIG. 19 illustrates an embodiment of a massively parallel array of a solid state molecular sensor device 190 comprising many TMD-containing enzyme polymerase structure (e.g. M0S2 or WS2 layer) for DNA or genome sequencing and label-free detection of nucleotide attachment. A TMD-containing enzyme polymerase molecular sensor 191 allows for label-free detection of nucleotide attachment. An areal distribution of the devices with associated routing of electrical wiring may be provided as illustrated. For example, Au lead wires 192 (surface insulated or coated to prevent protein adhesion) may be used. The availability of many parallel devices makes the sequencing analysis to be conducted faster, with more accuracy. Also, such a parallel processing scheme will make the overall system to be less costly.

FIG. 20 schematically illustrates operation of a microfluidic chamber wherein enzyme or other biomolecules are attached onto each TMD-containing molecular sensor device arranged in a massively parallel configuration. FIG. 20 illustrates a microfluidic reaction chamber 200 that is used to seed and attach biomolecules. In brief, this reaction chamber allows floating biomolecules 201 to be attached onto the exposed TMD islands, with unused biomolecules washed away through the chamber exit 202. In this operation, a phosphate- buffered saline (PBS) type aqueous solution 203 (or other solutions) containing enzymes or other biomolecules is supplied to a microfluidic reaction chamber 200. Individual single enzyme molecules are selectively attached with a high probability onto each of the size- limited, exposed TMD island regions 205 on the massive parallel sensor array. The probability of a single molecule attachment onto each TMD island is high because of the size-limited island configuration of the TMD, which is further enhanced because of the artificially and intentionally added, very large number of defects and more active binding sites such as the edge sites in nano-ribbons or in nanoporous layer TMD. In some embodiments, the success ratio of a single molecule adhesion to the available TMD island bridge locations is at least 30%, preferably at least 60%, and even more preferably at least 80%.

The unused biomolecules which did not adhere to the TMD islands are washed away out of the fluidic chamber. The analytes to be detected, such as nucleotides, DNA segments, or proteins, are then supplied into the chamber to attach to the enzyme polymerase to induce electrical signal pulse for biomolecule identification or DNA sequencing analysis.

Electrical connections for many parallel devices may be complex and take up device surface real estate space. One way of reducing the complexity and analysis time is to utilize a sequential interrogation of electrodes from the TMD-containing enzyme polymerase molecular sensor by using a common lead wire on one side of the array, as illustrated in FIG. 21, by shorting one side of all lead wires and taking turns with left side electrical lead wires one at a time, e.g., every millisecond, as shown in FIG. 21. This method has an advantage of requiring less electronic measurement complications of handling many thousands of parallel signals all at once.

FIG. 21 illustrates an embodiment of a TMD-containing enzyme polymerase molecular sensor for label-free detection or nucleotide detachment. A sequential interrogation of electrodes is applied from the TMD-containing enzyme polymerase molecular sensor 210 (e.g., with M0S2 or WS2 layer) for DNA or genome sequencing by using a common lead wire 211 on one side of the array. Au lead wires 212 are surface insulated or coated to prevent protein adhesion. All of the right side electrodes are connected as a common lead wire, whereas the left side electrodes are interrogated one at a time, sequentially.

Even larger data can be obtained if the sensor device structure, such as exemplified in

FIG. 19 or FIG. 21, is stacked in three dimension as shown in FIGS. 22A-22B, with accompanying microfluidic chambers for each stack (FIG. 22A) or using one or more common microfluidic chambers (FIG. 22B). FIGS. 22A-22B illustrate a three-dimensional array of molecular electronics genome-sequencing platform comprising TMD-based enzyme polymerase structure, e.g., with MoS2 or WS2 layers. An electrically insulating top coating (not shown) such as a polymer or an oxide layer (e.g., aluminum oxide, Si oxide, etc) is applied except in the exposed TMD region having an enzyme polymerase structure for nucleotide attachment. In some embodiments, there are 10 to 1,000 layers with each layer having, e.g., 100 to -10,000 devices in individualized microfluidic chambers with PBS solution and nucleotide control arrangements and an electronic sensing array. Fig 22 A illustrates an exemplary embodiment of one common microfluidic chamber 220 containing 10-1,000 layers, with each layer having, e.g., 100 to -10,000 devices. Each device layer has a multitude of molecular sensors 211. In such 3D configurations, at least one thousand to one million devices could be operated simultaneously for extremely rapid DNA or genome sequencing. For example, an electrically insulating top coating (not shown in FIGS. 22 A- 22B), such as a polymer or oxide coating (e.g. AI2O ₃ , S1O2, etc.), is applied over the surface except for the exposed TMD regions having the enzyme polymerase for nucleotide attachment. As illustrated in FIG. 22A, each 2D molecular electronics genome-sequencing device array is separately packaged into an individual microfluidic system 212. with each of the microfluidic layers stacked into a 3D configuration. In FIG. 22B, 2D molecular electronics genome-sequencing device arrays are stacked into 3D configurations but are housed in a single microfluidic system 213. The total number of molecular sensors can be at least 1,000, and can be as many as 1 million or more for massive parallel genome sequencing analysis.

When the sequencing device is not in use or being delivered or stored, it is important to make sure that the chamber is thoroughly washed and dried with a clean gas so that an adhesion or adsorption of unwanted gas molecules, dirt or dust in the form of nanoparticles and/or microparticles, is minimized. The sequencing device when not in use is desirably evacuated using a vacuum pump and back-filled with an inert gas so as to minimize the presence of unwanted gas molecules or dirt particles.

The overall genome or DNA sequencing system is described in FIG. 23 as a block flow diagram. Appropriate data analysis and storage software, computer systems (and Wi-Fi capability if desired) are incorporated, and microfluidic system is connected to the massively parallel electronic detection device array using the combined structure of TMD and single biomolecule enzyme polymerase, as well as coupling agents together with nucleotides to be sequenced. Instead of the desktop style units, portable or wearable units with information transfer or control via internet, Wi-Fi, cell phone or other methods can also be constructed and utilized. The high throughput DNA or genome sequencing device systems can be used for control, management and cure of diseases, as well as prediction and prevention of diseases from the genome sequence analysis for individual person.

The hierarchical process of nanofabrication, assembly and packaging of the device structures of FIG. 1A to FIG. 23 is desirably compatible with standard electronic device assembly such as c-MOS device fabrication and assembly. Parallel or areal processing steps, rather than individual processing steps, are thus preferred.

In some embodiments, the DNA or RNA molecular sensing device comprising modified or defective TMD structures such as MoS2 or WS2 is useful for partial or whole genome sequencing, or for diagnosis of diseases such as cancer. In some embodiments, the genome sequencing system can be operated as a desktop unit, a portable unit, or a wearable unit.

In some embodiments, the DNA or RNA molecular sensing device comprising modified or defective TMD structures such as M0S2 or WS2 is useful for partial or whole genome sequencing, or for diagnosis of diseases such as cancer. The genome sequencing system can be operated as a desktop unit, a portable unit or a wearable unit. Examples

Example 1: Method of Electron Beam (E-Beam) Patterning of M0S ₂ Layer using E- beam Lithography

M0S ₂ 300 is suspended or on a substrate 304 (FIG. 2A). A portion is of the M0S ₂ is subjected to an E-Beam 302. Resist is developed for nanopatterning (FIG. 2A). Chemical etch or Reactive Ion Etching is used to pattern the M0S ₂ (FIG. 2A). The resist is removed to pattern the MoS ₂ (FIG. 2A).

Example 2: Method of Nanoimprint Patterning of M0S ₂ layer

M0S ₂ 406 is suspended or on a substrate and resist material is applied to the M0S ₂

(FIG. 2B). A mold 400 is applied to nanoimprint the resist material 404 on the M0S ₂ layer (FIG. 2B). The mold is then released and reactive ion etching is applied to the resist material to form a nanopattern (FIG. 2B). Chemical etching or reactive ion etching is then used to pattern the M0S ₂ (FIG. 2B). The resist material is then removed to reveal the patterned M0S ₂ (FIG. 2B).

Example 3: Method of Synthesizing a Molecular Bridge of DNA or RNA Sensor comprising Size-Limited M0S ₂ Islands using Protective, Size-Limiting Dielectric Coating

A M0S ₂ (or TMD transition metal dichalcogenide) layer 36 is suspended over a conducting electrode pair 35 (Au, Pt, Ag, Pd, Rh, or their alloys, etc for signal detection) with a nanogap of e.g., 2-20 nm (FIG. 3B). The suspended M0S ₂ has a regular or narrow-ribbon configuration or it is intentionally made defective (FIG. 3B). If necessary, the M0S ₂ layer is patterned using an E-Beam or nanoimprinting (FIG. 3B). A protective, size-limiting dielectric coating 38 (e.g., polymer layer like PMMA or ceramic layer like S1O ₂ ) is added (FIG. 3C). The M0S ₂ is now size limited (e.g., 2-20 nm) for preferably a single biomolecule (e.g., polymerase enzyme) attachment (FIG. 3C). The Molecular bridge solid state sensor or M0S ₂ island can be used for genome or DNA sequencing via detection of change of current pulse or other signals upon attaching or detaching of nucleotide or other biomolecules (FIG. 3D).

Example 4: Method of Synthesizing a Molecular Bridge of a DNA or RNA Sensor comprising Size-Limited M0S ₂ Islands using an Intentionally Damaged TND region like M0S2 or WS ₂ A M0S ₂ (or TMD transition metal dichalcogenide) layer 56A is suspended over a conducting electrode pair 55 (Au, Pt, Ag, Pd, Rh, or their alloys, etc for signal detection) with a nanogap of e.g., 2-20 nm (FIG. 5B). The suspended M0S ₂ layer 56A (or transition metal dichalcogenide layer in general), has a regular structure or defective MoS2 (FIG. 5B). An intentionally damaged TND region like MoS ₂ or WS ₂ is applied 56B (FIG. 5C). The TND region can be processed by doping with ion implantation or by bombardment with electrons or other radiation, which converts it to an insulator or very high resistivity region to function as an effective mask to enable a single biomolecule (e.g., polymerase enzyme) attachment (FIG. 5D). The molecular bridge solid state sensor or M0S ₂ island can be used for genome or DNA sequencing via detection of change of current pulse or other signals upon attaching or detaching of nucleotide or other biomolecules (FIG. 5D).

Example 5: Method of Synthesizing a Molecular Bridge of DNA or RNA Sensor using a Suspended TMD Bridge

A suspended TMD bridge 66A is attached or affixed by van der Waals forces and a dielectric coating (FIG. 6A). A single enzyme molecule 61 (e.g., DNA or RNA polymerase) is attached onto the size limited TMD bridge 66A (FIG. 6A). A nucleotide monomer 65 is detected upon attachment to the DNA strand 63 due to a change in current that results from attachment (FIG. 6A).

Example 6: Method of Synthesizing a Molecular Bridge of DNA or RNA Sensor using a Substrate-Adhered M0S ₂ Bridge

A M0S ₂ layer 66B is substrate-adhered to the dielectric coating (FIG. 6B). A molecular bridge sensor with the TMD layer is affixed onto a dielectric substrate via van der Waals forces and a dielectric coating (FIG. 6B). A single enzyme molecule 61 (e.g., DNA or RNA polymerase) is attached onto the sized-limited TMD bridge (FIG. 6B). A nucleotide monomer 65 is detected upon attachment to the DNA strand due to a change in current that results from attachment (FIG. 6B). Example 7: Method of Synthesizing a Molecular Bridge of DNA or RNA Sensor by Connecting an Enzyme to a Suspended TMD Bridge via a Functionalization Group

An enzyme molecule 74 (e.g. DNA or RNA polymerase) is linked to a suspended TMD bridge 76 via a functionalizing group _ (FIG. 7A). A nucleotide monomer 73 is detected upon attachment of the monomer to the DNA strand 72 through a change in current (FIG. 7A).

Example 8: Method of Synthesizing a Molecular Bridge of DNA or RNA Sensor by Connecting an Enzyme to a Substrate- Adhered TMD Bridge via a Functionalization Group

An enzyme molecule 74 (e.g. DNA or RNA polymerase) is linked to a substrate- adhered TMD bridge 78 via a functionalization group TV (FIG. 7B). A nucleotide monomer 73 is detected upon attachment of the monomer to the DNA strand 72 through a change in current (FIG. 7B).

Example 9: Method of Producing Hydrophilic-Enabled TMS Bridge Surface Structures

A hydrophilic region is patterned or synthesized as a less perfect crystals 200 (e.g., -3-20 um width) (FIG. 10A). Alternatively, a composite configuration of a mix of hydrophilic and hydrophobic regions 202 can be produced (FIG. 10B). A TMD 204 (e.g., preferably defective or nanoporous (like MoS2 or WS2) sheet is masked by dielectric (e.g., PMMA or adhesion-impeding polymer layer) to prevent biomolecule attachment (FIGS. 10A and 10B). Conducting electrodes and lead wires 206 (Au, Pt, Ag, Pd, Rh, or their alloys) are used for signal detection (FIGS. 10A and 10B).

Example 10: Method of Producing a Nanopatterned TMD Bridge using a Diblock Copolymer Mask

A TMD like MoS ₂ or WS ₂ layer 130 is synthesized on metal foil 139 (e.g., by exfoliation, CVD or sulfurization of metal film) (FIG. 13 A). After the metal is etched away, the TMD layer is transferred onto a device surface, e.g., nano-gapped, Au, Pd, or Pt electrode pair on S1O ₂ 133 (or SiC^-coated Si substrate), to place the TMD layer as a suspended bridge (FIG. 13B). TMD is covered by a thin layer of evaporated S1O ₂ 134 and a thin film of spin- coated block-copolymer PS-b-P4VP 135 (FIG. 13C). The PS-b-P4VP block copolymer 135 film is annealed and developed into a nanoscale two-phase structure, leaving the porous PS matrix 136 as the template for subsequent patterning (FIG. 13D). Fluoride-based reactive ion etching (RIE) is used to penetrate and partem the S1O ₂ oxide layer, partially degrading the PS film, and forming the hard mask hole pattern 137 out of the thin S1O ₂ (FIG. 13E). The TMD layer in the exposed hole area is etched away by O ₂ plasma and then S1O ₂ is removed (FIG. 13F). The nanoporous TMD on SiO? 138 is obtained (FIG. 13F), which is then patterned into a limited size island TMD by dielectric masking for single molecule (e.g., enzyme) attachment. Example 11: Method of Producing a Nanopatterned TMD Bridge using an Anodized Aluminum Oxide (AAO) Membrane

A TMD like M0S ₂ or WS ₂ layer 140 is synthesized on metal foil (e.g., by exfoliation, CVD, or sulfurization of metal film) (FIG. 13G). The M0S ₂ layer is placed on a substrate 141 (FIG. 13H). An AAO nanohole membrane 142 is fabricated (FIG. 131). The AAO is placed on the M0S ₂ substrate 143 (FIG. 13 J). RIE etching of M0S ₂ is performed through the AAO holes 144 (FIG. 13K). A nanopatterned MoS ₂ 145 is created on the substrate after AAO mask removal (FIG. 13L).

Example 12: Method of Producing a Nanoporous TMD Bridge using an Incompletely Deposited Thin Film Mask

A thin TMD material like M0S ₂ or WS ₂ layer is synthesized by exfoliation, chemical vapor deposition (CVD), or sulfurization of metal film and placed on a substrate Support (sequencing structure base, or split substrates for M0S ₂ suspension. The M0S ₂ layer is deposited either by chemical vapor deposition (CVD) or by a transfer of pre-made M0S ₂ layer floating in aqueous or alcohol-containing solution onto a substrate by lifting up and drying. A thin film mask layer is then deposited on the top surface of M0S2, with a mask layer thickness of less than 5 nm, in an incomplete manner so that some nano regions are still not completely filled and nano-pinholes are present. The thin film is deposited by sputtering (other methods of deposition include evaporation, pulsed laser deposition or chemical deposition). The material for the thin film mask is selected from a ceramic layer such as S1O ₂ or a sputter depositable polymer such as polytetrafluoroethylene (PTFE) type polymer. The use of metallic thin film mask can also be used.

A relatively short period deposition of the thin film layer is performed so as to produce pinhole-containing, incomplete thin (less than 5 nm thick) film, with the pinhole size in the range of 0.5 - 5 nm average diameter, and a density of 10 ⁵ /cm ² or higher. An optional post-sputtering can also be applied to consolidate the pinholes to a more uniform sizes. In order to increase the pinhole type defects in sputter deposition, the thin film mask deposition is carried out preferentially at a lower temperature, preferably near or below room temperature.

The M0S2 layer underneath the thin film mask is then etched away through the mask defects by using either plasma etching (e.g., oxygen, CF4, SF6, or Ar plasma) or ion beam etching method. Chemical etching with an acid, e.g., selected from H2SO4, HNO ₃ , HC1 or their mixtures can also be utilized for M0S2 etching.

Once the nano-pinhole defects are prepared in the M0S2, the mask material is removed by selective chemical etching or plasma etching. The S1O2 type masks are readily removed by a BOE (buffered oxide etch) solution etching having a 6: 1 volume ratio of 40% NH ₄ F in water to 49% HF. The mask layer can also be etched away by plasma etching or ion beam etching. If NaCl or other salt type material is sputter deposited and employed as the mask layer, it can be dissolved away by water or solvents. Polymer mask films can be removed by solvent or by plasma etching.

The nano-pinhole defective M0S2 (or defective TMD materials in general) created by using such a thin film mask approach can be utilized for genome sequencing if they are prepared directly on M0S2 already mounted on a support (sequencing structure base, or split substrates for M0S2 suspension) by micro- or nano-patteming to have a limited-size bridge to enable a single molecule polymerase attachment. This is followed by nucleotide attachment analysis.

Alternatively, the defective M0S2 (or defective TMD materials) created by using such a thin film mask approach on a general substrate or dissolvable substrate can be released from the substrate by etching away, floating the M0S2 in a aqueous or alcohol-containing solution, picking up by the genome sequencing base structure and micro patterning into desired geometry.

A dielectric masking layer is placed on the defective M0S2 (or defective TMD materials). The defective M0S2 is created by using a thin film mask approach surface with a size-limited opening. This allows only a single enzyme biomolecule to attach onto the exposed M0S2 surface in a microfluidic system into which the DNA or genome sequencing structure is inserted. An electronic measurement and computer analysis are performed on attachment or detachment of a nucleotide monomer, a protein, a DNA segment, or other biomolecular component onto the enzyme polymerase molecule one at a time, which is then monitored to measure an electrical signal pulse and determine the specific nature of the nucleotide or biomolecules being attached. The embodiments and examples described above are only meant for exemplary purposes and are not meant to limit the scope of any of the embodiments described herein. Any equivalent modification or variation according to the spirit of any of the embodiments disclosed herein is to be also included within the scope of any of the embodiments disclosed herein.