Decoding DNA, RNA and peptides with quantum tunnelling

Length Discrimination of Homo-oligomeric Nucleic Acids with Single-molecule Measurement

Single-molecule DNA/RNA sequencing based on single-molecule measurement is a prominent method for higher throughput sequencing. In a previous report, the single-molecule DNA/RNA sequencing method has applied to detect each base-conductance difference in the tunneling current time profiles, and determined the sequence. However, discrimination of identical base lengths has not yet been achieved. The number of the identical contiguous bases has importance in biology because some homopolymers of nucleic acid control gene expression. In this study, we aimed to develop a method for discriminating the length of homopolymer of nucleic acids of adenosine monophosphate (AMP) using a single-molecule sequencing technique. We carried out single-molecule conductance measurements of adenine pentamer, hexamer and heptamer. The single-molecule signals of the oligomers are not distinguishable from current and duration time histograms. The three oligomers were discriminated by our developed machine learning-based analysis with accuracy of 0.54 for a single signal, and 99% for 40 signals. This method will be applied to the single signals and identify the contiguous bases in the sequence and provide new biological insights.

Advancing Biosensors with Machine Learning

Chemometrics play a critical role in biosensors-based detection, analysis, and diagnosis. Nowadays, as a branch of artificial intelligence (AI), machine learning (ML) have achieved impressive advances. However, novel advanced ML methods, especially deep learning, which is famous for image analysis, facial recognition, and speech recognition, has remained relatively elusive to the biosensor community. Herein, how ML can be beneficial to biosensors is systematically discussed. The advantages and drawbacks of most popular ML algorithms are summarized on the basis of sensing data analysis. Specially, deep learning methods such as convolutional neural network (CNN) and recurrent neural network (RNN) are emphasized. Diverse ML-assisted electrochemical biosensors, wearable electronics, SERS and other spectra-based biosensors, fluorescence biosensors and colorimetric biosensors are comprehensively discussed. Furthermore, biosensor networks and multibiosensor data fusion are introduced. This review will nicely bridge ML with biosensors, and greatly expand chemometrics for detection, analysis, and diagnosis.

Detection of an alcohol-associated cancer marker by single-molecule quantum sequencing

Alcoholic beverages are a well-known risk factor for cancer. N²-Ethyl-2'-deoxyguanosine (N²-Et-dG) is a promising biomarker for alcohol-associated cancers. However, the lack of a convenient detection method for N²-Et-dG hinders the development of practical DNA damage markers. Herein, we develop a detection method for N²-Et-dG using a single-molecule quantum sequencing (SMQS) method and machine learning analysis. Our method succeeded in discriminating between N²-Et-dG and dG with an accuracy of 99%, using 20 signals. Our developed method quantified the mixing ratio of N²-Et-dG from a mixed solution of N²-Et-dG and dG. It is shown that our method has the potential to facilitate the development of DNA damage markers, and thus the early detection and prevention of cancers.

Electrophoretic Transport of Single-Stranded DNA through a Two Dimensional Nanopore Patterned on an In-Plane Heterostructure

Recent advances in nanotechnology have facilitated fabrication of various solid state nanopores as a versatile alternative to biological nanopores; however, effective transport of a single-stranded DNA (ssDNA) molecule through solid state nanopores for sequencing has remained a challenge. In particular, the nonspecific interactions between the ssDNA and the engineered nanopore surface are known to impose difficulties on both transport and interrogation. Here, we show that a two-dimensional (2D) nanopore patterned on an in-plane heterostructure comprising both graphene and hexagonal boron nitride (hBN) can be utilized to transport the ssDNA electrophoretically. Energetically, a ssDNA molecule prefers to stay on the hBN domain than the graphene one since the former has a stronger van der Waals attraction with the ssDNA, as demonstrated in both classic molecular dynamics (MD) simulations and density functional theory (DFT) based calculations, which leads to the confinement of the ssDNA in the 2D nanopore. Therefore, this nanopore enables the manipulation of the conformation of a highly flexible ssDNA molecule on a flat 2D heterostructure surface, making it possible for sensing ssDNA bases using the high resolution atomic force microscopy (AFM) or scanning tunneling microscopy (STM) in the third dimension (perpendicular to the 2D surface).

Pore Structures for High-Throughput Nanopore Devices

Nanopore devices are expected to advance the next-generation of nanobiodevices because of their strong sensing and analyzing capabilities for single molecules and bioparticles. However, the device throughputs are not sufficiently high. Although analytes pass through a nanopore by electrophoresis, the electric field gradient is localized inside and around a nanopore structure. Thus, analytes located far from a nanopore cannot be driven by electrophoresis. Here, we report nanopore structures for high-throughput sensing, namely, inverted pyramid (IP)-shaped nanopore structures. Silicon-based IP-shaped nanopore structures create a homogeneous electric field gradient within a nanopore device, indicating that most of the analytes can pass through a nanopore by electrophoresis, even though the analytes are suspended far from the nanopore entrance. In addition, the nanostructures can be fabricated only by photolithography. The present study suggests a high potential for inverted pyramid shapes to serve as nanopore devices for high-throughput sensing.

Functionalized Nanogap for DNA Read-Out: Nucleotide Rotation and Current-Voltage Curves

Functionalized nanogaps embedded in nanopores show a strong potential for enhancing the detection of biomolecules, their length, type, and sequence. This detection is strongly dependent on the features of the target biomolecules, as well as the characteristics of the sensing device. In this work, through quantum-mechanical calculations, we elaborate on representative such aspects for the specific case of DNA detection and read-out. These aspects include the influence of single DNA nucleotide rotation within the nanogap and the current-voltage (I-V) characteristics of the nanogap. The results unveil a distinct variation in the electronic current across the functionalized device for the four natural DNA nucleotides with the applied voltage. These also underline the asymmetric response of the rotating nucleotides on this applied voltage and the respective variation in the rectification ratio of the device. The electronic tunneling current across the nanogap can be further enhanced through the proper choice of an applied bias voltage. We were able to correlate the enhancement of this current to the nucleotide rotation dynamics and a shift of the electronic transmission peaks towards the Fermi level. This nucleotide specific shift further reveals the sensitivity of the device in reading-out the identity of the DNA nucleotides for all different configurations in the nanogap. We underline the important information that can be obtained from both the I-V curves and the rectification characteristics of the nanogap device in view of accurately reading-out the DNA information. We show that tuning the applied bias can enhance this detection and discuss the implications in view of novel functionalized nanopore sequencers.

Key aurophilic motif for robust quantum-tunneling-based characterization of a nucleoside analogue marker

A quantum sequencer offers a scalable electrical platform for single-molecule analysis of genomic events. A thymidine (dT) analog exhibiting uniquely high single-molecule conductance is a key element in capturing DNA synthesis dynamics by serving as a decodable marker for enzymatic labeling of nascent strands. However, the current design strategies of dT analogs that focus on their molecular orbital energy levels require bulky chemical modifications to extend the π-conjugation, which hinders polymerase recognition. We report herein a polymerase-compatible dT analog that is highly identifiable in quantum sequencing. An ethynyl group is introduced as a small gold-binding motif to differentiate the nucleobase-gold electronic coupling, which has been an overlooked factor in modifying nucleobase conductance. The resulting C5-ethynyl-2'-deoxyuridine exhibits characteristic signal profiles that allowed its correct identification at a 93% rate while maintaining polymerase compatibility. This study would expand the applicability of quantum sequencing by demonstrating a robust nucleoside marker with high identifiability.

Critical Review: digital resolution biomolecular sensing for diagnostics and life science research

One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.

Time-resolved neurotransmitter detection in mouse brain tissue using an artificial intelligence-nanogap

The analysis of neurotransmitters in the brain helps to understand brain functions and diagnose Parkinson’s disease. Pharmacological inhibition experiments, electrophysiological measurement of action potentials, and mass analysers have been applied for this purpose; however, these techniques do not allow direct neurotransmitter detection with good temporal resolution by using nanometre-sized electrodes. Hence, we developed a method for direct observation of a single neurotransmitter molecule with a gap width of ≤ 1 nm and on the millisecond time scale. It consists of measuring the tunnelling current that flows through a single-molecule by using nanogap electrodes and machine learning analysis. Using this method, we identified dopamine, serotonin, and norepinephrine neurotransmitters with high accuracy at the single-molecule level. The analysis of the mouse striatum and cerebral cortex revealed the order of concentration of the three neurotransmitters. Our method will be developed to investigate the neurotransmitter distribution in the brain with good temporal resolution.

Planar graphene/h-BN/graphene heterostructures for protein stretching and confinement

Protein stretching and confinement in nanochannels is critical for advancing single-molecule detection techniques. For standard nanochannels integrated with nano-sensors, reducing their cross-section is beneficial for reading highly localized signals with minimal error, but results in increasing difficulty for the initial capture of any chain molecules due to the entropy barrier. Using molecular dynamics simulations, we show that spontaneous protein stretching can be realized by a two-dimensional (2D) heterostructure composed of a hexagonal boron nitride (h-BN) nanoribbon stitched with two graphene (GRA) sheets (i.e., a sandwiched GRA/BN/GRA structure). Due to fast protein diffusion on its flat surface and adsorption potential difference between two 2D materials, this planar nanochannel permits effective capture and elongation of three representative intrinsically disordered proteins including amyloid-β (1-42), polyglutamine (42) and α-synuclein (61-95). Moreover, we found that the extremely narrow h-BN stripe can provide stronger confinement for a longer polyglutamine chain after being stretched. Our approach has the potential to facilitate the bona fide readout of single-molecule protein sequencing techniques.

Integrating Artificial Intelligence and Nanotechnology for Precision Cancer Medicine

Artificial intelligence (AI) and nanotechnology are two fields that are instrumental in realizing the goal of precision medicine-tailoring the best treatment for each cancer patient. Recent conversion between these two fields is enabling better patient data acquisition and improved design of nanomaterials for precision cancer medicine. Diagnostic nanomaterials are used to assemble a patient-specific disease profile, which is then leveraged, through a set of therapeutic nanotechnologies, to improve the treatment outcome. However, high intratumor and interpatient heterogeneities make the rational design of diagnostic and therapeutic platforms, and analysis of their output, extremely difficult. Integration of AI approaches can bridge this gap, using pattern analysis and classification algorithms for improved diagnostic and therapeutic accuracy. Nanomedicine design also benefits from the application of AI, by optimizing material properties according to predicted interactions with the target drug, biological fluids, immune system, vasculature, and cell membranes, all affecting therapeutic efficacy. Here, fundamental concepts in AI are described and the contributions and promise of nanotechnology coupled with AI to the future of precision cancer medicine are reviewed.

Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements

In micro- and nanofluidic devices, liquid flows are often influenced by ionic currents generated by electric fields in narrow channels, which is an electrokinetic phenomenon. Various technologies have been developed that are analogous to semiconductor devices, such as diodes and field effect transistors. On the other hand, measurement techniques for local electric fields in such narrow channels have not yet been established. In the present study, electric fields in liquids are locally measured using glass micro-electrodes with 1-μm diameter tips, which are constructed by pulling a glass tube. By scanning a liquid poured into a channel by glass micro-electrodes, the potential difference in a liquid can be determined with a spatial resolution of the size of the glass tip. As a result, the electrical conductivity of sample solutions can be quantitatively evaluated. Furthermore, combining two glass capillaries filled with buffer solutions of different concentrations, an ionic diode that rectifies the proton conduction direction is constructed, and the possibility of pH measurement is also demonstrated. Under constant-current conditions, pH values ranging from 1.68 to 9.18 can be determined more quickly and stably than with conventional methods that depend on the proton selectivity of glass electrodes under equilibrium conditions.

Optimal in situ electromechanical sensing of molecular species

We investigate protocols for optimal molecular detection with electromechanical nanoscale sensors under ambient conditions. Our models are representative of suspended graphene nanoribbons, which due to their piezoelectric and electronic properties provide responsive and versatile sensors. In particular, we analytically account for the corrections in the electronic transmission function and signal-to-noise ratio originating in environmental perturbations, such as thermal fluctuations and solvation effects. We also investigate the role of the sampling time in the current statistics. As a result, we formulate a protocol for optimal sensing based on the modulation of the Fermi level at a fixed bias and provide approximate forms for the current, linear susceptibility, and current fluctuations. We show how the algebraic tails in the thermally broadened transmission function affect the behavior of the signal-to-noise ratio and optimal sensing. These results provide further insights into the operation of graphene deflectometers and other techniques for electromechanical sensing.

Combination of Single-Molecule Electrical Measurements and Machine Learning for the Identification of Single Biomolecules

The development of a next-generation DNA sequencer has provided a method for electrically measuring single molecules. Methods for electrically measuring one molecule are roughly divided into methods for measuring tunneling and ion currents. These methods enable identification of a single molecule of DNA, a RNA nucleotide, or a single protein based on current histograms. However, overlapping of current histograms of molecules with similar properties has been a major barrier to identifying single molecules with high accuracy. This barrier was broken by introducing machine learning. Combining single-molecule electrical measurement and machine learning enables high-precision identification of single molecules. Highly accurate discrimination has been demonstrated for DNA nucleotides, RNA nucleotides, amino acids, sugars, viruses, and bacteria. This combination enables quantitative evaluation of molecular recognition ability. Furthermore, a device structure suitable for high-precision identification has been designed. Combining single-molecule electrical measurement with machine learning enables digital analytical chemistry that can count certain types of molecules. Digital analytical chemistry enables comprehensive analysis of chemical reactions. This new analytical method will lead to the discovery of unknown or missed valuable molecules.

2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport

The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2'F-ANA. Moreover, we find that 2'F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2'F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine.

Chemical-Labeling-Assisted Detection of Nucleobase Modifications by Quantum-Tunneling-Based Single-Molecule Sensing

Quantum-tunneling-based DNA sensing is a single-molecule technique that promises direct mapping of nucleobase modifications. However, its applicability is seriously limited because of the small difference in conductivity between modified and unmodified nucleobases. Herein, a chemical labeling strategy is presented that facilitates the detection of modified nucleotides by quantum tunneling. We used 5-Formyl-2'-deoxyuridine as a model compound and demonstrated that chemical labeling dramatically alters its molecular conductance compared with that of canonical nucleotides; thus, facilitating statistical discrimination, which is impeded in the unlabeled state. This work introduces a chemical strategy that overcomes the intrinsic difficulty in quantum-tunneling-based modification analysis-the similarity of the molecular conductance of the nucleobases of interest.

Spontaneous ssDNA stretching on graphene and hexagonal boron nitride in plane heterostructures

Single-stranded DNA (ssDNA) molecules in solution typically form coiled structures, therefore stretching ssDNA is extremely crucial before applying any nanotechnology for ssDNA analysis. Recent advances in material fabrication enable the deployment of nanochannels to manipulate, stretch, sort and map double-stranded DNA (dsDNA) molecules, however nanochannels fail to stretch ssDNA molecules due to the ultra-short persistence length and the potential nonspecific-interaction-induced clogging. Given the significance of ssDNA stretching in genome analysis, here we report an ssDNA stretching platform: two dimensional in-plane heterostructure comprising graphene and hexagonal boron nitride (h-BN), and show that ssDNA can be stretched on a h-BN nanostripe sandwiched between two adjacent graphene domains (“nanochannel”). We further show that with a biasing voltage the stretched ssDNA can be electrophoretically transported along the “nanochannel”, allowing easy controls/manipulations. When being conveniently integrated with existing atomic resolution sensors, the heterostructure platform paves the way for sequencing DNA on a planar surface.

Single stranded DNA analysis is of interest for a range of applications; however, natural folding of DNA can cause problems with this. Here, the authors report on the in silico analysis of graphene and hexagonal-boron-nitride structures for the stretching and unfolding of DNA to allow for analysis.

Controlled current confinement in interfaced 2D nanosensor for electrical identification of DNA

The controlled synthesis of hybrid two-dimensional (2D) materials and the development of atomically precise nanopore fabrication techniques have opened up entirely new possibilities for sensing applications via nanoelectronics. Here, we investigate the electronic transport properties of an in-plane hybrid graphene/h-BN device, containing a graphene nanopore, to assess its feasibility to act as a molecular sensor. The results from our calculations based on density functional theory and the non-equilibrium Green's function formalism reveal the capability to confine the electric current pathways to the two carbon wires lining either edge of the nanopore, thereby creating conditions in which the conductance is highly sensitive to any changes in the electrical potential inside the nanopore. We apply this setup to assess whether it is possible to electrically determine the base sequence in a DNA molecule. Indeed, the modulation of the device conductance reveals a characteristic fingerprint of each nucleotide, which manifests itself in a pronounced difference in the sensitivity of the four different nucleotides, thereby allowing electrical discrimination. These findings lead us to propose this device architecture as a promising nanobiosensor. While fabrication in the lab may represent a profound experimental challenge, it should nevertheless in principle be feasible with existing contemporary techniques of hybrid 2D material synthesis, in conjunction with approaches for highly controlled nanopore creation.

Vibration assisted electron tunneling through nano-gaps in graphene nano-ribbons for amino-acid and peptide bond recognition

Peptide bond and amino-acid recognition by tunneling current flowing across nano-gaps of graphene nano-ribbons has been recently discussed. Theoretical predictions of the tunneling current signals were used in the elastic regime showing peculiar fingerprints. However, inelastic scattering due to vibrations is expected to play an important role. Then, the proposed strategy for peptide sequencing and amino-acid recognition is revised in the light of such inelastic scattering phenomena. Phonon and local vibrational mode assisted current tunneling is calculated by treating electron-phonon scattering in the context of the lowest order expansion of the self-consistent Born approximation. We study Gly and Ala homo-peptides as an example of very similar, small and neutral amino-acids that would be indistinguishable by means of standard techniques, such as the ionic blockade current, in real peptides. We show that all the inelastic contributions to the tunneling current are in the bias range 0 V ≤ V ≤ 0.5 V and that they can be classified, from an atomistic point of view, in terms of energy sub-ranges that they belong to. Peculiar fingerprints can be found for the typical configurations that have been recently found for peptide bond recognition by tunneling current.

Significant epitranscriptomes in heterogeneous cancer

Precision medicine places significant emphasis on techniques for the identification of DNA mutations and gene expression by deep sequencing of gene panels to obtain medical data. However, other diverse information that is not easily readable using bioinformatics, including RNA modifications, has emerged as a novel diagnostic and innovative therapy owing to its multifunctional aspects. It is suggested that this breakthrough innovation might open new avenues for the elucidation of uncharacterized cancer cellular functions to develop more precise medical applications. The functional characteristics and regulatory mechanisms of RNA modifications, ie, the epitranscriptome (ETR), which reflects RNA metabolism, remains unclear, mainly due to detection methods being limited. Recent studies have revealed that N6‐methyl adenosine, the most common modification in mRNA in eukaryotes, is affected in various types of cancer and, in some cases, cancer stem cells, but also affects cellular responses to viral infections. The ETR can control cancer cell fate through mRNA splicing, stability, nuclear export, and translation. Here we report on the recent progress of ETR detection methods, and biological findings regarding the significance of ETR in cancer precision medicine.

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.

Highly Conductive Nucleotide Analogue Facilitates Base-Calling in Quantum-Tunneling-Based DNA Sequencing

Quantum-tunneling-based DNA sequencing is a single molecular technology that has great potential for achieving facile and high-throughput DNA sequencing. In principle, the sequence of DNA could be read out by the time trace of the tunnel current that can be changed according to molecular conductance of nucleobases passing through nanosized gap electrodes. However, efficient base-calling of four genetic alphabets has been seriously impeded due to the similarity of molecular conductance among canonical nucleotides. In this article, we demonstrate that replacement of canonical 2'-deoxyadenosine (dA) with a highly conductive dA analogue, 7-deaza dA, could expand the difference of molecular conductance between four genetic alphabets. Additionally, systematic evaluation of molecular conductance using a series of dA and dG analogues revealed that molecular conductance of the nucleotide is highly dependent on the HOMO level. Thus, the present study demonstrating that signal characteristics of the nucleotide can be modulated based on the HOMO level provides a widely applicable chemical approach and insight for facilitation of single molecular sensing as well as DNA sequencing based on quantum tunneling.

Paving the way to single-molecule chemistry through molecular electronics

Since our understanding of single-molecule junctions, in which single molecules are connected between nanoelectrodes, has deepened, we have paved the way to single-molecule chemistry. Herein, we review fundamental properties, including the number of molecules connected to the electrode, their structure and type, the bonding force between the single molecule and electrode and the thermopower and quantum interference in single-molecule junctions. Additionally, we review the application of single-molecule junctions to biomolecules. Finally, we explore single-molecule chemical reaction analysis, which is one direction of single-molecule junction research.

Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations

Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.

Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates

In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.

Direct Analysis of Incorporation of an Anticancer Drug into DNA at Single-Molecule Resolution

Identifying positions at which anticancer drug molecules incorporate into DNA is essential to define mechanisms underlying their activity, but current methodologies cannot yet achieve this. The thymidine fluorine substitution product trifluridine (FTD) is a DNA-damaging anticancer agent thought to incorporate into thymine positions in DNA. This mechanism, however, has not been directly confirmed. Here, we report a means to detect FTD in a single-stranded oligonucleotide using a method to distinguish single molecules by differences in electrical conductance. Entire sequences of 21-base single-stranded DNAs with and without incorporated drug were determined based on single-molecule conductances of the drug and four deoxynucleosides, the first direct observation of its kind. This methodology may foster rapid development of more effective anticancer drugs.

Non-stationary analysis of molecule capture and translocation in nanopore arrays

Analytical formulas for the ON- and OFF-time distributions as well as for the autocorrelation function were derived for the case of single molecule translocation through nanopore arrays. The obtained time-dependent expressions describe very well experimentally recorded statistics of DNA translocations through an array of solid state nanopores, which allows us to extract molecule and system related physical parameters from the experimental traces. The necessity of non-stationary analysis as opposite to the steady-state approximation has been vindicated for the molecule capture process, where different time-dependent regimes were identified. A long tail in the distribution of translocation times has been rationalized invoking Markov jumps, where a possible sequential ordering of events was elucidated through autocorrelation function analysis.

Sub-5 nm Metal Nanogaps: Physical Properties, Fabrication Methods, and Device Applications

Sub-5 nm metal nanogaps have attracted widespread attention in physics, chemistry, material sciences, and biology due to their physical properties, including great plasmon-enhanced effects in light-matter interactions and charge tunneling, Coulomb blockade, and the Kondo effect under an electrical stimulus. These properties especially meet the needs of many cutting-edge devices, such as sensing, optical, molecular, and electronic devices. However, fabricating sub-5 nm nanogaps is still challenging at the present, and scaled and reliable fabrication, improved addressability, and multifunction integration are desired for further applications in commercial devices. The aim of this work is to provide a comprehensive overview of sub-5 nm nanogaps and to present recent advancements in metal nanogaps, including their physical properties, fabrication methods, and device applications, with the ultimate aim to further inspire scientists and engineers in their research.

Single-molecule protein sensing in a nanopore: a tutorial

Proteins are the structural elements and machinery of cells responsible for a functioning biological architecture and homeostasis. Advances in nanotechnology are catalyzing key breakthroughs in many areas, including the analysis and study of proteins at the single-molecule level. Nanopore sensing is at the forefront of this revolution. This tutorial review provides readers a guidebook and reference for detecting and characterizing proteins at the single-molecule level using nanopores. Specifically, the review describes the key materials, nanoscale features, and design requirements of nanopores. It also discusses general design requirements as well as details on the analysis of protein translocation. Finally, the article provides the background necessary to understand current research trends and to encourage the identification of new biomedical applications for protein sensing using nanopores.

Mechanically controlled quantum interference in graphene break junctions

The ability to detect and distinguish quantum interference signatures is important for both fundamental research and for the realization of devices such as electron resonators¹, interferometers² and interference-based spin filters³. Consistent with the principles of subwavelength optics, the wave nature of electrons can give rise to various types of interference effects⁴, such as Fabry-Pérot resonances⁵, Fano resonances⁶ and the Aharonov-Bohm effect⁷. Quantum interference conductance oscillations⁸ have, indeed, been predicted for multiwall carbon nanotube shuttles and telescopes, and arise from atomic-scale displacements between the inner and outer tubes^9,10. Previous theoretical work on graphene bilayers indicates that these systems may display similar interference features as a function of the relative position of the two sheets^11,12. Experimental verification is, however, still lacking. Graphene nanoconstrictions represent an ideal model system to study quantum transport phenomena^13-15 due to the electronic coherence¹⁶ and the transverse confinement of the carriers¹⁷. Here, we demonstrate the fabrication of bowtie-shaped nanoconstrictions with mechanically controlled break junctions made from a single layer of graphene. Their electrical conductance displays pronounced oscillations at room temperature, with amplitudes that modulate over an order of magnitude as a function of subnanometre displacements. Surprisingly, the oscillations exhibit a period larger than the graphene lattice constant. Charge-transport calculations show that the periodicity originates from a combination of the quantum interference and lattice commensuration effects of two graphene layers that slide across each other. Our results provide direct experimental observation of a Fabry-Pérot-like interference of electron waves that are partially reflected and/or transmitted at the edges of the graphene bilayer overlap region.

Nucleotide and structural label identification in single RNA molecules with quantum tunneling spectroscopy

Although a number of advances have been made in RNA sequencing and structural characterization, the lack of a method for directly determining the sequence and structure of single RNA molecules has limited our ability to probe heterogeneity in gene expression at the level of single cells. Here we present a method for direct nucleotide identification and structural label mapping of single RNA molecules via Quantum Molecular Sequencing (QMSeq). The method combines non-perturbative quantum tunneling spectroscopy to probe the molecular orbitals of ribonucleotides, new experimental biophysical parameters that fingerprint these molecular orbitals, and a machine learning classification algorithm to distinguish between the ribonucleotides. The algorithm uses tunneling spectroscopy measurements on an unknown ribonucleotide to determine its chemical identity and the presence of local chemical modifications. Combining this with structure-dependent chemical labeling presents the possibility of mapping both the sequence and local structure of individual RNA molecules. By optimizing the base-calling algorithm, we show a high accuracy for both ribonucleotide discrimination (>99.8%) and chemical label identification (>98%) with a relatively modest molecular coverage (35 repeat measurements). This lays the groundwork for simultaneous sequencing and structural mapping of single unknown RNA molecules, and paves the way for probing the sequence-structure-function relationship within the transcriptome at an unprecedented level of detail.

Scalable Manufacturing of Nanogaps

The ability to manufacture a nanogap in between two electrodes has proven a powerful catalyst for scientific discoveries in nanoscience and molecular electronics. A wide range of bottom-up and top-down methodologies are now available to fabricate nanogaps that are less than 10 nm wide. However, most available techniques involve time-consuming serial processes that are not compatible with large-scale manufacturing of nanogap devices. The scalable manufacturing of sub-10 nm gaps remains a great technological challenge that currently hinders both experimental nanoscience and the prospects for commercial exploitation of nanogap devices. Here, available nanogap fabrication methodologies are reviewed and a detailed comparison of their merits is provided, with special focus on large-scale and reproducible manufacturing of nanogaps. The most promising approaches that could achieve a breakthrough in research and commercial applications are identified. Emerging scalable nanogap manufacturing methodologies will ultimately enable applications with high scientific and societal impact, including high-speed whole genome sequencing, electromechanical computing, and molecular electronics using nanogap electrodes.

The present and future of de novo whole-genome assembly

As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome.

Asymmetric Nafion-Coated Nanopore Electrode Arrays as Redox-Cycling-Based Electrochemical Diodes

Inspired by the functioning of cellular ion channels, pore-based structures with nanoscale openings have been fabricated and integrated into ionic circuits, for example, ionic diodes and transistors, for signal processing and detection. In these systems, the nonlinear current responses arise either because asymmetric nanopore geometries break the symmetry of the ion distribution, creating unequal surface charge across the nanopore, or by coupling unidirectional electron transfer within a nanopore electrode. Here we develop a high-performance redox-cycling-based electrochemical diode by coating an asymmetric ion-exchange membrane, that is, Nafion, on the top surface of a nanopore electrode array (Nafion@NEA), in which each pore in the array exhibits one or more annular electrodes. Nafion@NEAs exhibit highly sensitive and charge-selective electroanalytical measurements due to efficient redox-cycling reaction, the permselectivity of Nafion, and the strong confinement of redox species in the nanopore array. In addition, the top electrode of dual-electrode Nafion@NEAs can serve as a voltage-controlled switch to gate ion transport within the nanopore. Thus Nafion@NEAs can be operated as a diode by switching voltages applied to the top and bottom electrodes of the NEA, leading to a large rectification ratio, fast response times, and simplified circuitry without the need for external electrodes. By taking advantage of closely spaced and individually addressable electrodes, the redox-cycling electrochemical diode has the potential for application to large-scale production and electrochemically controlled circuit operations, which go well beyond conventional electronic diodes or transistors.

Sequencing nothing: Exploring failure modes of nanopore sensing and implications for life detection

The detection of extant life is a major focus of many planned future planetary missions, a current challenge of which is the ability to target biomarkers capable of providing unambiguous evidence of life. DNA sequencing is increasingly recognized as a powerful tool for life detection for planetary exploration missions; beyond use of sequence information to determine the origins of the sample (e.g., extant life or forward contamination), recent advances in the field have enabled interrogation of single molecules, with or without amplification. The focus of this work is on failure modes, specifically the issues encountered when there is no-to-low input DNA into a sequencing device, and the potential for the generation of sequencing artifacts that could be interpreted as a false positive. Using Oxford Nanopore Technologies (ONT) MinION, we assess whether single molecule sequencing, involving no amplification, generates noise signals that could be misinterpreted in the context of a planetary exploration mission, and also whether the ability of the instrument to handle these types of situations could make it feasible for clean room monitoring. Utilizing quality score filtering techniques in place at the time of this experiment, runs containing only initial flowcell chemistry and/or library reagents generated 5 passing reads out of a total of 3568 measured reads, and contained estimated sequences with low complexity that did not map to the NCBI database. The noise characteristics in all instances suggest that quality thresholds were appropriately chosen by ONT: new chemistry and basecalling workflows have shown further suppression of noise sources, which completely mitigate the generation of spurious reads.

Quantitative analysis of DNA with single-molecule sequencing

Cancer can be diagnosed by identifying DNA and microRNA base sequences that have the same base length yet differ in a few base sequences, if the abundance ratios of these slightly deviant base sequences can be determined. However, such quantitative analyses cannot be performed using the current DNA sequencers. Here we determine entire base sequences of four types of DNA corresponding to the let-7 microRNA, which is a 22-base cancer marker. We record the single-molecule conductances of the base molecules using current-tunneling measurements. In addition, we count the numbers of molecules in a solution to determine the abundance ratios of two DNA strands that differ by a single base sequence.

Nitrogen Doping of Carbon Nanoelectrodes for Enhanced Control of DNA Translocation Dynamics

Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures and for achieving this goal, herein, we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs. We find that the substitutional nitrogen doping of capCNTs facilitates and stabilizes the edge-on nucleobase configurations rather than the original face-on ones and slows down the DNA translocation speed by establishing hydrogen bonds between the N dopant atoms and nucleobases. Due to the enhanced interactions between DNAs and N-doped capCNTs, the duration time of nucleobases within the nanogap was extended by up to ∼300%. Given the possibility to be combined with the extrinsic light or gate voltage modulation methods, the current work demonstrates that the substitutional nitrogen doping is a promising direction for the control of DNA translocation dynamics through a nanopore or nanogap, based of carbon nanomaterials.

Protein sequencing via nanopore based devices: a nanofluidics perspective

Proteins perform a huge number of central functions in living organisms, thus all the new techniques allowing their precise, fast and accurate characterization at single-molecule level certainly represent a burst in proteomics with important biomedical impact. In this review, we describe the recent progresses in the developing of nanopore based devices for protein sequencing. We start with a critical analysis of the main technical requirements for nanopore protein sequencing, summarizing some ideas and methodologies that have recently appeared in the literature. In the last sections, we focus on the physical modelling of the transport phenomena occurring in nanopore based devices. The multiscale nature of the problem is discussed and, in this respect, some of the main possible computational approaches are illustrated.

High spatial resolution nanoslit SERS for single-molecule nucleobase sensing

Solid-state nanopores promise a scalable platform for single-molecule DNA analysis. Direct, real-time identification of nucleobases in DNA strands is still limited by the sensitivity and the spatial resolution of established ionic sensing strategies. Here, we study a different but promising strategy based on optical spectroscopy. We use an optically engineered elongated nanopore structure, a plasmonic nanoslit, to locally enable single-molecule surface enhanced Raman spectroscopy (SERS). Combining SERS with nanopore fluidics facilitates both the electrokinetic capture of DNA analytes and their local identification through direct Raman spectroscopic fingerprinting of four nucleobases. By studying the stochastic fluctuation process of DNA analytes that are temporarily adsorbed inside the pores, we have observed asynchronous spectroscopic behavior of different nucleobases, both individual and incorporated in DNA strands. These results provide evidences for the single-molecule sensitivity and the sub-nanometer spatial resolution of plasmonic nanoslit SERS.

Direct and real-time identification of nucleobases in DNA strands is still limited by the sensitivity and spatial resolution of the established solid-state nanopore devices. Here, the authors use CMOS compatible, plasmonic nanoslits to locally enable SERS for identifying nucleobases, both individual and incorporated in DNA strands.

Quantitative Evaluation of Dielectric Breakdown of Silicon Micro- and Nanofluidic Devices for Electrophoretic Transport of a Single DNA Molecule

In the present study, we quantitatively evaluated dielectric breakdown in silicon-based micro- and nanofluidic devices under practical electrophoretic conditions by changing the thickness of the insulating layer. At higher buffer concentration, a silicon nanofluidic device with a 100 nm or 250 nm silicon dioxide layer tolerated dielectric breakdown up to ca. 10 V/cm, thereby allowing successful electrophoretic migration of a single DNA molecule through a nanochannel. The observed DNA migration behavior suggested that parameters, such as thickness of the insulating layer, tolerance of dielectric breakdown, and bonding status of silicon and glass substrate, should be optimized to achieve successful electrophoretic transport of a DNA molecule through a nanopore for nanopore-based DNA sequencing applications.

Nanocracking and metallization doubly defined large-scale 3D plasmonic sub-10 nm-gap arrays as extremely sensitive SERS substrates

Considering the technological difficulties in the existing approaches to form nanoscale gaps, a convenient method to fabricate three-dimensional (3D) sub-10 nm Ag/SiN_x gap arrays has been demonstrated in this study, controlled by a combination of stress-induced nanocracking of a SiN_x nanobridge and Ag nanofilm deposition. This scalable 3D plasmonic nanogap is specially suspended above a substrate, having a tunable nanogap width and large height-to-width ratio to form a nanocavity underneath. As a surface-enhanced Raman scattering (SERS) substrate, the 3D Ag/SiN_x nanogap shows a large Raman enhancement factor of ∼10⁸ and extremely high sensitivity for the detection of Rhodamine 6G (R6G) molecules, even down to 10^-16 M, indicating an extraordinary capability for single-molecule detection. Further, we verified that the Fabry-Perot resonance occurred in the deep SiN_x nanocavity under the Ag nanogap and contributed prominently to a tremendous enhancement of the local field in the Ag-nanogap zone and hence ultrasensitive SERS detection. This method circumvents the technological limitations to fabricate a sub-10 nm metal nanogap with unique features for wide applications in important scientific and technological areas.

Non-invasive lung disease diagnostics from exhaled microdroplets of lung fluid: perspectives and technical challenges

The combination of ultra-sensitive assay techniques and recent improvements in the instrumentation used to collect microdroplets of lung fluid (MLF) from exhaled breath has enabled the development of non-invasive lung disease diagnostics that are based on MLF analysis. In one example of this approach, electrospun nylon filters were used to collect MLFs from patients with pulmonary tuberculosis. The filters were washed to obtain liquid probes, which were then tested for human immunoglobulin A (h-IgA) and fractions of h-IgA specific to ESAT-6 and Psts-1, two antigens secreted by Mycobacterium tuberculosis. Probes collected for 10 min contained 100-1500 fg of h-IgA and, in patients with pulmonary tuberculosis, a portion of these h-IgA molecules showed specificity to the secreted antigens. Separate MLFs and their dry residues were successfully collected using an electrostatic collector and impactor developed especially for this purpose. Visualization of MLF dry residues by atomic force microscopy made it possible to estimate the lipid content in each MLF and revealed mucin molecules in some MLFs. This exciting new approach will likely make it possible to detect biomarkers in individual MLFs. MLFs emerging from an infection site ('hot' microdroplets) are expected to be enriched with infection biomarkers. This paper discusses possible experimental approaches to detecting biomarkers in single MLFs, as well as certain technological problems that need to be resolved in order to develop new non-invasive diagnostics based on analysing biomarkers in separate MLFs.

Enhancing the sensitivity of DNA detection by structurally modified solid-state nanopore

Solid-state nanopore is an ionic current-based biosensing platform, which would be a top candidate for next-generation DNA sequencing and a high-throughput drug-screening tool at single-molecular-scale resolution. There have been several approaches to enhance the sensitivity and reliability of biomolecule detection using the nanopores particularly in two aspects: signal-to-noise ratio (SNR) and translocation dwell time. In this study, an additional nano-well of 100-150 nm diameter and the aspect ratio of ∼5 called 'guide structure' was inserted in conventional silicon-substrate nanopore device to increase both SNR and dwell time. First, the magnitude of signals (conductance drop (ΔG)) increased 2.5 times under applied voltage of 300 mV through the guide-inserted nanopore compared to the conventional SiN/Si nanopore in the same condition. Finite element simulation was conducted to figure out the origin of ΔG modification, which showed that the guide structure produced high ΔG due to the compartmental limitation of ion transports through the guide to the sensing nanopore. Second, the translocation velocity decreased in the guide-inserted structure to a maximum of 20% of the velocity in the conventional device at 300 mV. Electroosmotic drag formed inside the guide structure, when directly applied to the remaining segment of translocating DNA molecules in cis chamber, affected the DNA translocation velocity. This study is the first experimental report on the effect of the geometrical confinement to a remnant DNA on both SNR and dwell time of nanopore translocations.

Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection

In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN _x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.