Identification of DNA basepairing via tunnel-current decay

Insight of Employing Molecular Junctions for Sensor Applications

Molecular junctions (MJs) exhibit distinct charge transport properties and have the potential to become the next generation of electronic devices. Advancing molecular electronics for practical uses, such as sensors, is crucial to propel its progress to the next level. In this review, we discussed how MJs can serve as a sensor for detecting a wide range of analytes with exceptional sensitivity and specificity. The primary advances and potential of molecular junctions for the various kinds of sensors including photosensors, explosives (DNTs, TNTs), cancer biomarker detection (DNA, mRNA), COVID detection, biogases (CO, NO, NH), environmental pH, practical chemicals, and water pollutants are listed and examined here. The fundamental ideas of molecular junction formation as well as the sensing mechanism have been examined here. This review demonstrates that MJ-based sensors hold significant promise for real-time and on-site detection. It provides valuable insights into current research and outlines potential future directions for advancing molecular junction-based sensors for practical applications.

The Protein Matrix of Plastocyanin Supports Long-Distance Charge Transport with Photosystem I and the Copper Ion Regulates Its Spatial Span and Conductance

Charge exchange is the fundamental process that sustains cellular respiration and photosynthesis by shuttling electrons in a cascade of electron transfer (ET) steps between redox cofactors. While intraprotein charge exchange is well characterized in protein complexes bearing multiple redox sites, interprotein processes are less understood due to the lack of suitable experimental approaches and the dynamic nature of the interactions. Proteins constrained between electrodes are known to support electron transport (ETp) through the protein matrix even without redox cofactors, as the charges housed by the redox sites in ET are furnished by the electrodes. However, it is unknown whether protein ETp mechanisms apply to the interprotein medium present under physiological conditions. We study interprotein charge exchange between plant photosystem I (PSI) and its soluble redox partner plastocyanin (Pc) and address the role of the Pc copper center. Using electrochemical scanning tunneling spectroscopy (ECSTS) current-distance and blinking measurements, we quantify the spatial span of charge exchange between individual Pc/PSI pairs and ETp through transient Pc/PSI complexes. Pc devoid of the redox center (Pcapo) can exchange charge with PSI at longer distances than with the copper ion (Pcholo). Conductance bursts associated with Pcapo/PSI complex formation are higher than in Pcholo/PSI. Thus, copper ions are not required for long-distance Pc/PSI ETp but regulate its spatial span and conductance. Our results suggest that the redox center that carries the charge in Pc is not necessary to exchange it in interprotein ET through the aqueous solution and question the canonical view of tight complex binding between redox protein partners.

Robust Single-Supermolecule Switches Operating in Response to Two Different Noncovalent Interactions

Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.

Chemical Sensors using Single-Molecule Electrical Measurements

Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.

Distance and Potential Dependence of Charge Transport Through the Reaction Center of Individual Photosynthetic Complexes

Charge separation and transport through the reaction center of photosystem I (PSI) is an essential part of the photosynthetic electron transport chain. A strategy is developed to immobilize and orient PSI complexes on gold electrodes allowing to probe the complex's electron acceptor side, the chlorophyll special pair P700. Electrochemical scanning tunneling microscopy (ECSTM) imaging and current-distance spectroscopy of single protein complex shows lateral size in agreement with its known dimensions, and a PSI apparent height that depends on the probe potential revealing a gating effect in protein conductance. In current-distance spectroscopy, it is observed that the distance-decay constant of the current between PSI and the ECSTM probe depends on the sample and probe electrode potentials. The longest charge exchange distance (lowest distance-decay constant β) is observed at sample potential 0 mV/SSC (SSC: reference electrode silver/silver chloride) and probe potential 400 mV/SSC. These potentials correspond to hole injection into an electronic state that is available in the absence of illumination. It is proposed that a pair of tryptophan residues located at the interface between P700 and the solution and known to support the hydrophobic recognition of the PSI redox partner plastocyanin, may have an additional role as hole exchange mediator in charge transport through PSI.

Nanopore chip with self-aligned transverse tunneling junction for DNA detection

To achieve better signal quality and resolution in nanopore sequencing, there has been strong interest in quantum tunneling based detection which requires integration of tunneling junctions in nanopores. However, there has been very limited success due to precision and reproducibility issues. Here we report a new strategy based on feedback-controlled electrochemical processes in a confined nanoscale space to construct nanopore devices with self-aligned transverse tunneling junctions, all embedded on a nanofluidic chip. We demonstrate high-yield (>93%) correlated detection of translocating DNAs from both the ionic channel and the tunneling junction with enriched event rate. We also observed events attributed to non-translocating DNA making contact with the transverse electrodes. Existing challenges for precise sequencing are discussed, including fast translocation speed, and interference from transient electrostatic signals from fast-moving DNAs. Our work can serve as a first step to provide an accessible, and reproducible platform enabling further optimizations for tunneling-based DNA detection, and potentially sequencing.

Identifying DNA Nucleotides via Transverse Electronic Transport in Atomically Thin Topologically Defected Graphene Electrodes

Extended line defects in graphene (ELDG) sheets have been found to be promising for biomolecule sensing applications. By means of the consistent-exchange van der Waals density-functional (vdW-DF-cx) method, the electronic, structural, and quantum transport properties of the ELDG nanogap setup has been studied when a DNA nucleotide molecule is positioned inside the nanogap electrodes. The interaction energy (E_i) values indicate charge transfer interaction between the nucleotide molecule and electrode edges. The charge density difference plots reveal that charge fluctuates around the ELDG nanogap edges adjacent to the nucleotides. This charge redistribution grounds the modulation of electronic charge transport in the ELDG nanogap device. Further, we study the electronic transverse-conductance and tunnelling current-voltage (I-V) characteristics across two closely spaced ELDG nanogap electrodes using the density functional theory and the nonequilibrium Green's function methods when a DNA nucleotide is translocated through the nanogap. Our outcomes indicate that the ELDG nano gap device could allow sequencing of DNA nucleotides with a robust and consistent yield, giving the tunneling electric current signals that vary by more than 1 order of magnitude electric current (I) for the different DNA nucleotides. So, we predict that the ELDG nanogap-based tunneling device can be suitable for sequencing DNA nucleobases.

Functionalized carbon nanotube electrodes for controlled DNA sequencing

In the last decade, solid-state nanopores/nanogaps have attracted significant attention in the rapid detection of DNA nucleotides. However, reducing the noise through controlled translocation of the DNA nucleobases is a central issue for the development of nanogap/nanopore-based DNA sequencing to achieve single-nucleobase resolution. Furthermore, the high reactivity of the graphene pores/gaps causes clogging of the pore/gap, leading to the blockage of the pores/gaps, sticking, and irreversible pore closure. To address the prospective of functionalization of the carbon nanostructure and for accomplishing this objective, herein, we have studied the performance of functionalized closed-end cap armchair carbon nanotube (CNT) nanogap-embedded electrodes, which can improve the coupling through non-bonding electrons and may provide the possibility of N/O-H⋯π interactions with the nucleotides, as single-stranded DNA is transmigrated across the electrode. We have investigated the effect of functionalizing the closed-end cap CNT (6,6) electrodes with purine (adenine, guanine) and pyrimidine (thymine, cytosine) molecules. Weak hydrogen bonds formed between the probe molecule and the target DNA nucleobase enhance the electronic coupling and temporarily stabilize the translocating nucleobase against the orientational fluctuations, which may reduce noise in the current signal during experimental measurements. The findings of our density functional theory and non-equilibrium Green's function-based study indicate that this modeled setup could allow DNA nucleotide sequencing with a better and reliable yield, giving current traces that differ by at least 1 order of current magnitude for all the four target nucleotides. Thus, we feel that the functionalized armchair CNT (6,6) nanogap-embedded electrodes may be utilized for controlled DNA sequencing.

The influence of a solvent on the electronic transport across diamondoid-functionalized biosensing electrodes

Electrodes embedded in nanopores have the potential to detect the identity of biomolecules, such as DNA. This identification is typically being done through electronic current measurements across the electrodes in a solvent. In this work, using quantum-mechanical calculations, we qualitatively present the influence of this solvent on the current signals. For this, we model electrodes functionalized with a small diamond-like molecule known as diamondoid and place a DNA nucleotide within the electrode gap. The influence of an aqueous solvent is taken explicitly into account through Quantum-Mechanics/Molecular Mechanics (QM/MM) simulations. From these, we could clearly reveal that at the (111) surface of the Au electrode, water molecules form an adlayer-like structure through hydrogen bond networks. From the temporal evolution of the hydrogen bond between a nucleotide and the functionalizing diamondoid, we could extract information on the conductance across the device. In order to evaluate the influence of the solvent, we compare these results with ground-state electronic structure calculations in combination with the non-equilibrium Green's function (NEGF) approach. These allow access to the electronic transport across the electrodes and show a difference in the detection signals with and without the aqueous solution. We analyze the results with respect to the density of states in the device. In the end, we demonstrate that the presence of water does not hinder the detection of a mutation over a healthy DNA nucleotide. We discuss these results in view of sequencing DNA with nanopores.

Quantum Point Contact Single-Nucleotide Conductance for DNA and RNA Sequence Identification

Several nanoscale electronic methods have been proposed for high-throughput single-molecule nucleic acid sequence identification. While many studies display a large ensemble of measurements as "electronic fingerprints" with some promise for distinguishing the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine, and uracil), important metrics such as accuracy and confidence of base calling fall well below the current genomic methods. Issues such as unreliable metal-molecule junction formation, variation of nucleotide conformations, insufficient differences between the molecular orbitals responsible for single-nucleotide conduction, and lack of rigorous base calling algorithms lead to overlapping nanoelectronic measurements and poor nucleotide discrimination, especially at low coverage on single molecules. Here, we demonstrate a technique for reproducible conductance measurements on conformation-constrained single nucleotides and an advanced algorithmic approach for distinguishing the nucleobases. Our quantum point contact single-nucleotide conductance sequencing (QPICS) method uses combed and electrostatically bound single DNA and RNA nucleotides on a self-assembled monolayer of cysteamine molecules. We demonstrate that by varying the applied bias and pH conditions, molecular conductance can be switched ON and OFF, leading to reversible nucleotide perturbation for electronic recognition (NPER). We utilize NPER as a method to achieve >99.7% accuracy for DNA and RNA base calling at low molecular coverage (∼12×) using unbiased single measurements on DNA/RNA nucleotides, which represents a significant advance compared to existing sequencing methods. These results demonstrate the potential for utilizing simple surface modifications and existing biochemical moieties in individual nucleobases for a reliable, direct, single-molecule, nanoelectronic DNA and RNA nucleotide identification method for sequencing.

Single Nucleobase Identification Using Biophysical Signatures from Nanoelectronic Quantum Tunneling

Nanoelectronic DNA sequencing can provide an important alternative to sequencing-by-synthesis by reducing sample preparation time, cost, and complexity as a high-throughput next-generation technique with accurate single-molecule identification. However, sample noise and signature overlap continue to prevent high-resolution and accurate sequencing results. Probing the molecular orbitals of chemically distinct DNA nucleobases offers a path for facile sequence identification, but molecular entropy (from nucleotide conformations) makes such identification difficult when relying only on the energies of lowest-unoccupied and highest-occupied molecular orbitals (LUMO and HOMO). Here, nine biophysical parameters are developed to better characterize molecular orbitals of individual nucleobases, intended for single-molecule DNA sequencing using quantum tunneling of charges. For this analysis, theoretical models for quantum tunneling are combined with transition voltage spectroscopy to obtain measurable parameters unique to the molecule within an electronic junction. Scanning tunneling spectroscopy is then used to measure these nine biophysical parameters for DNA nucleotides, and a modified machine learning algorithm identified nucleobases. The new parameters significantly improve base calling over merely using LUMO and HOMO frontier orbital energies. Furthermore, high accuracies for identifying DNA nucleobases were observed at different pH conditions. These results have significant implications for developing a robust and accurate high-throughput nanoelectronic DNA sequencing technique.

A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing

We propose an aqueous functionalized molybdenum disulfide nanoribbon suspended over a solid electrode as a capacitive displacement sensor aimed at determining the DNA sequence. The detectable sequencing events arise from the combination of Watson-Crick base-pairing, one of nature's most basic lock-and-key binding mechanisms, with the ability of appropriately sized atomically thin membranes to flex substantially in response to subnanonewton forces. We employ carefully designed numerical simulations and theoretical estimates to demonstrate excellent (79% to 86%) raw target detection accuracy at ∼70 million bases per second and electrical measurability of the detected events. In addition, we demonstrate reliable detection of repeated DNA motifs. Finally, we argue that the use of a nanoscale opening (nanopore) is not requisite for the operation of the proposed sensor and present a simplified sensor geometry without the nanopore as part of the sensing element. Our results, therefore, potentially suggest a realistic, inherently base-specific, high-throughput electronic DNA sequencing device as a cost-effective de novo alternative to the existing methods.

Side-gated ultrathin-channel nanopore FET sensors

A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing

We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions.

Strong Fermi level pinning induces a high rectification ratio and negative differential resistance in hydrogen bonding bridged single cytidine pair junctions

Strong Fermi level pinning induces a high rectification ratio and negative differential resistance in hydrogen bonding bridged single cytidine pair junctions.

DNA sequencing by two-dimensional materials: As theoretical modeling meets experiments

Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, two-dimensional (2D) materials (mainly including graphene, boron nitride, MoS₂ etc.) have stimulated exploding interests in sensor applications. 2D-material based nanoscale DNA sequencing is a single-molecule technique with revolutionary potential. In this paper, we review the methodology of DNA sequencing based on the measurements of ionic current, force peak, and transverse electrical currents etc. by 2D materials. The advantages and disadvantages of DNA sequencing by 2D materials are discussed. Besides the recent development of experiments, we will focus on the theoretical calculations of DNA sequencing, which have been played a critical role in the development of this field. Special emphasis will focus on the disagreements between experiments and theoretical calculations, and the explanations for the discrepancy will be highlighted. Finally, some new plausible sequencing methods from computational studies will be discussed, which may be applied in the realistic DNA sequencing experiments in future.

Threading DNA through nanopores for biosensing applications

This review outlines the recent achievements in the field of nanopore research. Nanopores are typically used in single-molecule experiments and are believed to have a high potential to realize an ultra-fast and very cheap genome sequencer. Here, the various types of nanopore materials, ranging from biological to 2D nanopores are discussed together with their advantages and disadvantages. These nanopores can utilize different protocols to read out the DNA nucleobases. Although, the first nanopore devices have reached the market, many still have issues which do not allow a full realization of a nanopore sequencer able to sequence the human genome in about a day. Ways to control the DNA, its dynamics and speed as the biomolecule translocates the nanopore in order to increase the signal-to-noise ratio in the reading-out process are examined in this review. Finally, the advantages, as well as the drawbacks in distinguishing the DNA nucleotides, i.e., the genetic information, are presented in view of their importance in the field of nanopore sequencing.

Correlation of breaking forces, conductances and geometries of molecular junctions

Electrical and mechanical properties of elongated gold-molecule-gold junctions formed by tolane-type molecules with different anchoring groups (pyridyl, thiol, amine, nitrile and dihydrobenzothiophene) were studied in current-sensing force spectroscopy experiments and density functional simulations. Correlations between forces, conductances and junction geometries demonstrate that aromatic tolanes bind between electrodes as single molecules or as weakly-conductive dimers held by mechanically-weak π - π stacking. In contrast with the other anchors that form only S-Au or N-Au bonds, the pyridyl ring also forms a highly-conductive cofacial link to the gold surface. Binding of multiple molecules creates junctions with higher conductances and mechanical strengths than the single-molecule ones.

Challenges in DNA motion control and sequence readout using nanopore devices

Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport.

Recent progress in atomistic simulation of electrical current DNA sequencing

We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices.

The evolution of nanopore sequencing

The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

Fabrication and characterization of nanopores with insulated transverse nanoelectrodes for DNA sensing in salt solution

We report on the fabrication, simulation, and characterization of insulated nanoelectrodes aligned with nanopores in low-capacitance silicon nitride membrane chips. We are exploring these devices for the transverse sensing of DNA molecules as they are electrophoretically driven through the nanopore in a linear fashion. While we are currently working with relatively large nanopores (6-12 nm in diameter) to demonstrate the transverse detection of DNA, our ultimate goal is to reduce the size sufficiently to resolve individual nucleotide bases, thus sequencing DNA as it passes through the pore. We present simulations and experiments that study the impact of insulating these electrodes, which is important to localize the sensing region. We test whether the presence of nanoelectrodes or insulation affects the stability of the ionic current flowing through the nanopore, or the characteristics of DNA translocation. Finally, we summarize the common device failures and challenges encountered during fabrication and experiments, explore the causes of these failures, and make suggestions on how to overcome them in the future.

Control of DNA capture by nanofluidic transistors

We report the use of an array of electrically gated ~200 nm solid-state pores as nanofluidic transistors to manipulate the capture and passage of DNA. The devices are capable of reversibly altering the rate of DNA capture by over 3 orders of magnitude using sub-1 V biasing of a gate electrode. This efficient gating originates from the counter-balance of electrophoresis and electroosmosis, as revealed by quantitative numerical simulations. Such a reversible electronically tunable biomolecular switch may be used to manipulate nucleic acid delivery in a fluidic circuit, and its development is an important first step toward active control of DNA motion through solid-state nanopores for sensing applications.

Solid-state nanopores for biosensing with submolecular resolution

Biological cell membranes contain various types of ion channels and transmembrane pores in the 1–100 nm range, which are vital for cellular function. Individual channels can be probed electrically, as demonstrated by Neher and Sakmann in 1976 using the patch-clamp technique [Neher and Sakmann (1976) Nature 260, 799–802]. Since the 1990s, this work has inspired the use of protein or solid-state nanopores as inexpensive and ultrafast sensors for the detection of biomolecules, including DNA, RNA and proteins, but with particular focus on DNA sequencing. Solid-state nanopores in particular have the advantage that the pore size can be tailored to the analyte in question and that they can be modified using semi-conductor processing technology. This establishes solid-state nanopores as a new class of single-molecule biosensor devices, in some cases with submolecular resolution. In the present review, we discuss a few of the most important recent developments in this field and how they might be applied to studying protein–protein and protein–DNA interactions or in the context of ultra-fast DNA sequencing.

Single-molecule electrical random resequencing of DNA and RNA

Two paradigm shifts in DNA sequencing technologies—from bulk to single molecules and from optical to electrical detection—are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5′-UGAGGUA-3′ from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

Transistor-like behavior of single metalloprotein junctions

Single protein junctions consisting of azurin bridged between a gold substrate and the probe of an electrochemical tunneling microscope (ECSTM) have been obtained by two independent methods that allowed statistical analysis over a large number of measured junctions. Conductance measurements yield (7.3 ± 1.5) × 10(-6)G(0) in agreement with reported estimates using other techniques. Redox gating of the protein with an on/off ratio of 20 was demonstrated and constitutes a proof-of-principle of a single redox protein field-effect transistor.

Long lifetime of hydrogen-bonded DNA basepairs by force spectroscopy

Electron-tunneling data suggest that a noncovalently-bonded complex of three molecules, two recognition molecules that present hydrogen-bond donor and acceptor sites via a carboxamide group, and a DNA base, remains bound for seconds. This is surprising, given that imino-proton exchange rates show that basepairs in a DNA double helix open on millisecond timescales. The long lifetime of the three-molecule complex was confirmed using force spectroscopy, but measurements on DNA basepairs are required to establish a comparison with the proton-exchange data. Here, we report on a dynamic force spectroscopy study of complexes between the bases adenine and thymine (A-T, two-hydrogen bonds) and 2-aminoadenine and thymine (2AA-T, three-hydrogen bonds). Bases were tethered to an AFM probe and mica substrate via long, covalently linked polymer tethers. Data for bond-survival probability versus force and the rupture-force distributions were well fitted by the Bell model. The resulting lifetime of the complexes at zero pulling force was ~2 s for two-hydrogen bonds (A-T) and ~4 s for three-hydrogen bonds (2AA-T). Thus, DNA basepairs in an AFM pulling experiment remain bonded for long times, even without the stabilizing influence of base-stacking in a double helix. This result suggests that the pathways for opening, and perhaps the open states themselves, are very different in the AFM and proton-exchange measurements.

Electrochemical protection of thin film electrodes in solid state nanopores

Solid state nanopores are a core element of next-generation single molecule tools in the field of nano-biotechnology. Thin film electrodes integrated into a pore can interact with charges and fields within the pore. In order to keep the nanopore open and thus functional electrochemically induced surface alteration of electrode surfaces and bubble formation inside the pore have to be eliminated. This paper provides electrochemical analyses of nanopores drilled into TiN membranes which in turn were employed as thin film electrodes. We studied physical pore integrity and the occurrence of water decomposition yielding bubble formation inside pores by applying voltages between -4.5 and +4.5 V to membranes in various protection stages continuously for up to 24 h. During potential application pores were exposed to selected electrolyte-solvent systems. We have investigated and successfully eliminated electrochemical pore oxidation and reduction as well as water decomposition inside nanopores of various diameters ranging from 3.5 to 25 nm in 50 nm thick TiN membranes by passivating the nanopores with a plasma-oxidized layer and using a 90% solution of glycerol in water as KCl solvent. Nanopore ionic conductances were measured before and after voltage application in order to test for changes in pore diameter due to electrochemical oxidation or reduction. TEM imaging was used to confirm these observations. While non-passivated pores were electrochemically oxidized, neither electrochemical oxidation nor reduction was observed for passivated pores. Bubble formation through water decomposition could be detected in non-passivated pores in KCl/water solutions but was not observed in 90% glycerol solutions. The use of a protective self-assembled monolayer of hexadecylphosphonic acid (HDPA) was also investigated.

Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes

Protein nanopores may provide a cheap and fast technology to sequence individual DNA molecules. However, the electrophoretic translocation of ssDNA molecules through protein nanopores has been too rapid for base identification. Here, we show that the translocation of DNA molecules through the α-hemolysin protein nanopore can be slowed controllably by introducing positive charges into the lumen of the pore by site directed mutagenesis. Although the residual ionic current during DNA translocation is insufficient for direct base identification, we propose that the engineered pores might be used to slow down DNA in hybrid systems, for example, in combination with solid-state nanopores.

DNA tunneling detector embedded in a nanopore

We report on the fabrication and characterization of a DNA nanopore detector with integrated tunneling electrodes. Functional tunneling devices were identified by tunneling spectroscopy in different solvents and then used in proof-of-principle experiments demonstrating, for the first time, concurrent tunneling detection and ionic current detection of DNA molecules in a nanopore platform. This is an important step toward ultrafast DNA sequencing by tunneling.

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

Recognition tunneling

Single molecules in a tunnel junction can now be interrogated reliably using chemically functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ('tethered molecule-pair' configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the 'free-analyte' configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules.

Charge transport in DNA oligonucleotides with various base-pairing patterns

We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.

Identifying single nucleotides by tunnelling current

A major goal in medical research is to develop a DNA sequencing technique that is capable of reading an entire human genome at low cost. Recently, it was proposed that DNA sequencing could be performed by measuring the electron transport properties of the individual nucleotides in a DNA molecule. Here, we report electrical detection of single nucleotides using two configurable nanoelectrodes and show that electron transport through single nucleotides occurs by tunnelling. We also demonstrate statistical identification of the nucleotides based on their electrical conductivity, thereby providing an experimental basis for a DNA sequencing technology based on measurements of electron transport.

Electronic signatures of all four DNA nucleosides in a tunneling gap

Nucleosides diffusing through a 2 nm electron-tunneling junction generate current spikes of sub-millisecond duration with a broad distribution of peak currents. This distribution narrows 10-fold when one of the electrodes is functionalized with a reagent that traps nucleosides in a specific orientation with hydrogen bonds. Functionalizing the second electrode reduces contact resistance to the nucleosides, allowing them to be identified via their peak currents according to deoxyadenosine > deoxycytidine > deoxyguanosine > thymidine, in agreement with the order predicted by a density functional calculation.

The next-generation sequencing technology: a technology review and future perspective

As one of the most powerful tools in biomedical research, DNA sequencing not only has been improving its productivity in an exponential growth rate but also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades. In this technical review, we look into technical characteristics of the next-gen sequencers and provide prospective insights into their future development and applications. We envisage that some of the emerging platforms are capable of supporting the $1000 genome and $100 genome goals if given a few years for technical maturation. We also suggest that scientists from China should play an active role in this campaign that will have profound impact on both scientific research and societal healthcare systems.

Single-molecule DNA analysis

The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

Perspectives and challenges of emerging single-molecule DNA sequencing technologies

The growing demand for analysis of the genomes of many species and cancers, for understanding the role of genetic variation among individuals in disease, and with the ultimate goal of deciphering individual human genomes has led to the development of non-Sanger reaction-based technologies towards rapid and inexpensive DNA sequencing. Recent advancements in new DNA sequencing technologies are changing the scientific horizon by dramatically accelerating biological and biomedical research and promising an era of personalized medicine for improved human health. Two single-molecule sequencing technologies based on fluorescence detection are already in a working state. The newly launched and emerging single-molecule DNA sequencing approaches are reviewed here. The current challenges of these technologies and potential methods of overcoming these challenges are critically discussed. Further research and development of single-molecule sequencing will allow researchers to gather nearly error-free genomic data in a timely and inexpensive manner.

Real-time detection of deoxyribonucleic acid bases via their negative differential conductance signature

In this Brief Report, we present a method for the real-time detection of the bases of the deoxyribonucleic acid using their signatures in negative differential conductance measurements. The present methods of electronic detection of deoxyribonucleic acid bases are based on a statistical analysis because the electrical currents of the four bases are weak and do not differ significantly from one base to another. In contrast, we analyze a device that combines the accumulated knowledge in nanopore and scanning tunneling detection and which is able to provide very distinctive electronic signatures for the four bases.

Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise

The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break.

Tunnelling readout of hydrogen-bonding-based recognition

Hydrogen bonding has a ubiquitous role in electron transport and in molecular recognition, with DNA base pairing being the best-known example. Scanning tunnelling microscope images and measurements of the decay of tunnel current as a molecular junction is pulled apart by the scanning tunnelling microscope tip are sensitive to hydrogen-bonded interactions. Here, we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA base pairs. Junctions that are held together by three hydrogen bonds per base pair (for example, guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per base pair (for example, adenine-thymine interactions). Similar, but less pronounced effects are observed on the approach of the tunnelling probe, implying that attractive forces that depend on hydrogen bonds also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal.

Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing

We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact's Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green's-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.

Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore

The sequencing of individual DNA strands with nanopores is under investigation as a rapid, low-cost platform in which bases are identified in order as the DNA strand is transported through a pore under an electrical potential. Although the preparation of solid-state nanopores is improving, biological nanopores, such as alpha-hemolysin (alphaHL), are advantageous because they can be precisely manipulated by genetic modification. Here, we show that the transmembrane beta-barrel of an engineered alphaHL pore contains 3 recognition sites that can be used to identify all 4 DNA bases in an immobilized single-stranded DNA molecule, whether they are located in an otherwise homopolymeric DNA strand or in a heteropolymeric strand. The additional steps required to enable nanopore DNA sequencing are outlined.

Transverse field effects on DNA-sized particle dynamics

We report the development of microfluidics-integrated mechanically controllable break junction device and its applications to electrical characterizations of DNA-sized particle dynamics in a microfluidic channel. It is found that the electrostatic electrode-particle interaction slows down the particle flow through the electrode nanogaps. The present results suggest the useful capability of transverse electric field for controlling DNA translocations through a nanopore.

A hydrogen-bonded electron-tunneling circuit reads the base composition of unmodified DNA

Using a tunnel junction in which one electrode is guanidinium-functionalized (to trap DNA via hydrogen bonding to the backbone phosphates) and a second electrode which is functionalized with a base (to capture its complementary target on the DNA), current versus distance curves are obtained which yield an accurate measure of the base composition of DNA oligomers. With this long tunneling path, resolution is limited to sequence blocks of about twenty bases or larger, because of the need to form a large-area tunnel junction. A shorter hydrogen-bonded path across bases will be required for DNA sequencing. Nonetheless, these measurements point the way to a new type of nanoscale sensor.

Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH(2))(2))-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

The potential and challenges of nanopore sequencing

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for approximately $1,000 in approximately 24 h.