Tuning the Electromechanical Properties of Single DNA Molecular Junctions

Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements

The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.

Molecular Electronics: Creating and Bridging Molecular Junctions and Promoting Its Commercialization

Molecular electronics is driven by the dream of expanding Moore's law to the molecular level for next-generation electronics through incorporating individual or ensemble molecules into electronic circuits. For nearly 50 years, numerous efforts have been made to explore the intrinsic properties of molecules and develop diverse fascinating molecular electronic devices with the desired functionalities. The flourishing of molecular electronics is inseparable from the development of various elegant methodologies for creating nanogap electrodes and bridging the nanogap with molecules. This review first focuses on the techniques for making lateral and vertical nanogap electrodes by breaking, narrowing, and fixed modes, and highlights their capabilities, applications, merits, and shortcomings. After summarizing the approaches of growing single molecules or molecular layers on the electrodes, the methods of constructing a complete molecular circuit are comprehensively grouped into three categories: 1) directly bridging one-molecule-electrode component with another electrode, 2) physically bridging two-molecule-electrode components, and 3) chemically bridging two-molecule-electrode components. Finally, the current state of molecular circuit integration and commercialization is discussed and perspectives are provided, hoping to encourage the community to accelerate the realization of fully scalable molecular electronics for a new era of integrated microsystems and applications.

Characterization and Application of Supramolecular Junctions

The convergence of supramolecular chemistry and single-molecule electronics offers a new perspective on supramolecular electronics, and provides a new avenue toward understanding and application of intermolecular charge transport at the molecular level. In this review, we will provide an overview of the advances in the characterization technique for the investigation of intermolecular charge transport, and summarize the experimental investigation of several non-covalent interactions, including π-π stacking interactions, hydrogen bonding, host-guest interactions and σ-σ interactions at the single-molecule level. We will also provide a perspective on supramolecular electronics and discuss the potential applications and future challenges.

Measurements of single-molecule electromechanical properties based on atomic force microscopy fixed-junction technique

A hybrid technique combining atomic force microscopy and the fixed-junction technique is developed to simultaneously probe the electrical and mechanical characteristics of a single-molecule junction.

Hard-Soft Chemistry Guides the Adaptable Charge Transport in Lysine-doped Heptapeptide Junctions

Counterions always coexist with charged peptides in charge transport process, which are excellent candidate components for tunable molecular electronic devices. Here, we introduced hard-soft acid base theory to analyze the...

Fine-tuning the DNA conductance by intercalation of drug molecules

In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.

Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963-2020)

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.

Ballistic transport and quantum unfurling in molecular junctions via minimal representations of quantum master equations

Quantum furling and unfurling are inelastic transitions between localized and delocalized electronic states. We predict scenarios where these processes govern charge transport through donor-bridge-acceptor molecular junctions. Like in the case of ballistic transport, the resulting currents are nearly independent of the molecular bridge length. However, currents involving quantum furling and unfurling processes can be controlled by the coupling to vibrations in the intra-molecular and the extra-molecular environment, which can be experimentally tuned. Our study is based on rate equations for exchange of energy (bosons) and particles (fermions) between the molecular bridge and its environment. An efficient algorithm is introduced for a compact representation of the relevant rate equations, which utilizes the redundancies in the rate matrix and the sparsity of the creation and annihilation operators in the molecular Fock space.

Tuning molecular fluctuation to boost the conductance in DNA based molecular wires

Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na⁺ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.

Generalized Voigt broadening due to thermal fluctuations of electromechanical nanosensors and molecular electronic junctions

Graphene and other 2D materials give a platform for electromechanical sensing of biomolecules in aqueous, room temperature environments. The electronic current changes in response to mechanical deflection, indicating the presence of forces due to interactions with, e.g., molecular species. We develop illustrative models of these sensors in order to give explicit, compact expressions for the current and signal-to-noise ratio. Electromechanical structures have an electron transmission function that follows a generalized Voigt profile, with thermal fluctuations giving a Gaussian smearing analogous to thermal Doppler broadening in solution/gas-phase spectroscopic applications. The Lorentzian component of the profile comes from the contact to the electrodes. After providing an accurate approximate form of this profile, we calculate the mechanical susceptibility for a representative two-level bridge and the current fluctuations for electromechanical detection. These results give the underlying mechanics of electromechanical sensing in more complex scenarios, such as graphene deflectometry.

High-Voltage-Assisted Mechanical Stabilization of Single-Molecule Junctions

Resonant tunneling is an efficient mechanism for charge transport through nanoscale conductance junctions due to the relatively high currents involved. However, continuous charging and discharging cycles of the nanoconductor during resonant tunneling often lead to mechanical instability. The realization of efficient nanoscale electronic components therefore depends to a large extent on the ability to mechanically stabilize them during resonant transport. In this work, we focus on single-molecule junctions, demonstrating that their mechanical stability during resonant transport can be increased by increasing the bias voltage. This counter-intuitive effect is attributed to the energy dependence of the molecule-lead coupling densities, which promote the rate of transport-induced cooling of molecular vibrations at higher voltages. The required energy dependence is characteristic of realistic electrodes (such as graphene), which cannot be modeled within the commonly invoked wide-band approximation. Our research provides new guidelines for the design of mechanically stable molecular devices operating in the regime of resonant charge transport and demonstrates these guidelines while considering realistic features of single-molecule junctions.

DNA-Based Single-Molecule Electronics: From Concept to Function

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

Gate-controlled conductance switching in DNA

Extensive evidence has shown that long-range charge transport can occur along double helical DNA, but active control (switching) of single-DNA conductance with an external field has not yet been demonstrated. Here we demonstrate conductance switching in DNA by replacing a DNA base with a redox group. By applying an electrochemical (EC) gate voltage to the molecule, we switch the redox group between the oxidized and reduced states, leading to reversible switching of the DNA conductance between two discrete levels. We further show that monitoring the individual conductance switching allows the study of redox reaction kinetics and thermodynamics at single molecular level using DNA as a probe. Our theoretical calculations suggest that the switch is due to the change in the energy level alignment of the redox states relative to the Fermi level of the electrodes.

Thanks to its base stacking structure, DNA can behave as an electric wire, but external control of its electronic properties has not been achieved yet. Here, the authors show that DNA conductance can be switched electrochemically when a DNA base is replaced by the redox molecule anthraquinone.

Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break.