Direct measurement of electrical transport through single DNA molecules of complex sequence

DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics

Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.

Non-Faradaic Impedimetric Detection of Heavy Metal Ions via a Hybrid Nanoparticle-DNAzyme Biosensor

Due to rapid industrialization, novel water-quality monitoring techniques for the detection of highly toxic and hazardous heavy metal ions are essential. Herein, a hybrid noble nanoparticle/DNAzyme electrochemical biosensor is proposed for the simultaneous and label-free detection of Pb2+ and Cr3+ in aqueous solutions. The sensor is based on the combination of a two-dimensional naked-platinum nanoparticle film and DNAzymes, whose double-helix configuration disassembles into smaller fragments in the presence of target-specific heavy metal ions. The electrochemical behavior of the fabricated sensor was investigated with non-faradaic electrochemical impedance spectroscopy (EIS), resulting in the successful detection of Pb2+ and Cr3+ well below their maximum permitted levels in tap water. So far, there has been no report on the successful detection of heavy metal ions utilizing the non-faradaic electrochemical impedance spectroscopy technique based on advanced nanomaterials paired with DNAzymes. This is also one of the few reports on the successful detection of chromium (III) via a sensor incorporating DNAzymes.

Chemical Repair of Radical Damage to the GC Base Pair by DNA-Bound Bisbenzimidazoles

The migration of an electron-loss center (hole) in calf thymus DNA to bisbenzimidazole ligands bound in the minor groove is followed by pulse radiolysis combined with time-resolved spectrophotometry. The initially observed absorption spectrum upon oxidation of DNA by the selenite radical is consistent with spin on cytosine (C), as the GC• pair neutral radical, followed by the spectra of oxidized ligands. The rate of oxidation of bound ligands increased with an increase in the ratio (r) ligands per base pair from 0.005 to 0.04. Both the rate of ligand oxidation and the estimated range of hole transfer (up to 30 DNA base pairs) decrease with the decrease in one-electron reduction potential between the GC• pair neutral radical of ca. 1.54 V and that of the ligand radicals (E0', 0.90-0.99 V). Linear plots of log of the rate of hole transfer versus r give a common intercept at r = 0 and a free energy change of 12.2 ± 0.3 kcal mol-1, ascribed to the GC• pair neutral radical undergoing a structural change, which is in competition to the observed hole transfer along DNA. The rate of hole transfer to the ligands at distance, R, from the GC• pair radical, k2, is described by the relationship k2 = k0 exp(constant/R), where k0 includes the rate constant for surmounting a small barrier.

Review of the Role of Nanotechnology in Overcoming the Challenges Faced in Oral Cancer Diagnosis and Treatment

Throughout the world, oral cancer is a common and aggressive malignancy with a high risk of morbidity, mortality, and recurrence. The importance of early detection in cancer prevention and disease treatment cannot be overstated. Conventional therapeutic strategies have minor difficulties but considerable side effects and unfavourable consequences in clinical applications. Hence, there is a requirement for effective ways for early detection and treatment of oral cancer. At present, numerous forms of nanoparticles have piqued researchers' interest as a potentially useful tool for diagnostic probes and medicinal devices. Because of their inherent physicochemical properties and customizable surface modification, they are able to circumvent some of restrictions and accomplish the intended diagnostic and therapeutic impact. Nanotechnology is a unique field that has revolutionised the industry and is paving the way for new treatments for oral cancer. It can help with a better diagnosis with less harmful substances and is setting current guidelines for treatment. The use of nanotechnology in cancer diagnosis, therapy, and care improves clinical practise dramatically. The different types of nanoparticles that have been developed for the diagnosis and therapy of oral cancers will be covered in this study. The difficulties and potential uses of nanoparticles in the treatment and diagnosis of oral cancer are then highlighted. In order to emphasise existing difficulties and potential remedies for oral cancer, a prospective view of the future is also provided.

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.

Reversible Regulation of Long-Distance Charge Transport in DNA Nanowires by Dynamically Controlling Steric Conformation

Understanding of DNA-mediated charge transport (CT) is significant for exploring circuits at the molecular scale. However, the fabrication of robust DNA wires remains challenging due to the persistence length and natural flexibility of DNA molecules. Moreover, CT regulation in DNA wires often relies on predesigned sequences, which limit their application and scalability. Here, we addressed these issues by preparing self-assembled DNA nanowires with lengths of 30-120 nm using structural DNA nanotechnology. We employed these nanowires to plug individual gold nanoparticles into a circuit and measured the transport current in nanowires with an optical imaging technique. Contrary to the reported cases with shallow or no length dependence, a fair current attenuation was observed with increasing nanowire length, which experimentally confirmed the prediction of the incoherent hopping model. We also reported a mechanism for the reversible CT regulation in DNA nanowires, which involves dynamic transitions in the steric conformation.

Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA

DNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the sodium ion (Na^{+}), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment in charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.

Towards atom manufacturing with framework nucleic acids

Atom manufacturing has become a blooming frontier direction in the field of material and chemical science in recent years, focusing on the fabrication of functional materials and devices with individual atoms or with atomic precision. Framework nucleic acids (FNAs) refer to nanoscale nucleic acid framework structures with novel properties distinct from those of conventional nucleic acids. Due to their ability to be precisely positioned and assembled at the nanometer or even atomic scale, FNAs are ideal materials for atom manufacturing. They hold great promise for the bottom-up construction of electronic devices by precisely arranging and integrating building blocks with atomic or near-atomic precision. In this review, we summarize the progress of atom manufacturing based on FNAs. We begin by introducing the atomic-precision construction of FNAs and the intrinsic electrical properties of DNA molecules. Then, we describe various approaches for the fabrication of FNAs templated materials and devices, which are classified as conducting, insulating, or semiconducting based on their electrical properties. We highlight the role of FNAs in the fabrication of functional electronic devices with atomic precision, as well as the challenges and opportunities for atom manufacturing with FNAs.

Response of electron transfer capacity of humic substances to soil microenvironment

The humic substances (HS) - mediated electron transfer process is of great significance to the reduction and degradation of pollutants and the improvement of soil quality. Different soil conditions lead to different characteristics of HS, resulting in differences in the electron transfer capacity (ETC) of HS. It is unclear how the environmental conditions in soil affect the ETC by affecting on HS. In this study, the response relationship of soil microenvironment, HS and ETC has been studied. The results show that the ETC follows the descending order of: Langshan > Nanchang > Anqing > Beijing > Guilin. There were significant differences in ETC in soil HS in different regions. There were significant differences in electron-donating capacity (EDC) in soil HS in different regions and depths. EDC in soil was higher than electron-accepting capacity (EAC), and on average, are 22.4 times higher than the EAC. The HS components of soils in different regions are different. The most significant differences were in tyrosine-like substances and soluble microbial by-products (SMPs). The five components of the soil HS from Langshan were the most different from those in other regions. There were differences in SMPs and humic-like substances in soils of different depths in Anqing and Guilin. ETC can be affected by the composition of HS components in different regions. The composition of HS at different soil depths in the same regions had little effect on ETC. SMPs can promote ETC and EDC, and tyrosine-like substance can promote EDC. Moisture content, pH and TOC are the main factors affecting the composition of HS components. This results can provide a research basis for the sustainable and safe utilization of agricultural soil.

Charge transfer mechanisms in DNA at finite temperatures: From quasiballistic to anomalous subdiffusive charge transfer

We address various regimes of charge transfer in DNA within the framework of the Peyrard-Bishop-Holstein model and analyze them from the standpoint of the characteristic size and timescales of the electronic and vibrational subsystems. It is demonstrated that a polaron is an unstable configuration within a broad range of temperatures and therefore polaronic contribution to the charge transport is irrelevant. We put forward an alternative fluctuation-governed charge transfer mechanism and show that the charge transfer can be quasiballistic at low temperatures, diffusive or mixed at intermediate temperatures, and subdiffusive close to the DNA denaturation transition point. Dynamic fluctuations in the vibrational subsystem is the key ingredient of our proposed mechanism which allows for explanation of all charge transfer regimes at finite temperatures. In particular, we demonstrate that in the most relevant regime of high temperatures (above the aqueous environment freezing point), the electron dynamics is completely governed by relatively slow fluctuations of the mechanical subsystem. We argue also that our proposed analysis methods and mechanisms can be relevant for the charge transfer in other organic systems, such as conjugated polymers, molecular aggregates, α-helices, etc.

Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity

Detection of molecular interactions is the foundation for many important biotechnology applications in society and industry, such as drug discovery, diagnostics, and DNA sequencing. This report describes a broadly applicable platform for detecting molecular interactions at the single-molecule scale, in real-time, label-free, and potentially highly multiplexable fashion, using single-molecule sensors on a highly scalable semiconductor sensor array chip. Such chips are both practically manufacturable in the near term, and have a durable long-term scaling roadmap, thus providing an ideal way to bring the power of modern chip technology to the broad area of biosensing. This work also realizes a 50-year-old scientific vision of integrating single molecules into electronic chips to achieve the ultimate miniaturization of electronics.

For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.

Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions

Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.

Single-molecule junction spontaneously restored by DNA zipper

The electrical properties of DNA have been extensively investigated within the field of molecular electronics. Previous studies on this topic primarily focused on the transport phenomena in the static structure at thermodynamic equilibria. Consequently, the properties of higher-order structures of DNA and their structural changes associated with the design of single-molecule electronic devices have not been fully studied so far. This stems from the limitation that only extremely short DNA is available for electrical measurements, since the single-molecule conductance decreases sharply with the increase in the molecular length. Here, we report a DNA zipper configuration to form a single-molecule junction. The duplex is accommodated in a nanogap between metal electrodes in a configuration where the duplex is perpendicular to the nanogap axis. Electrical measurements reveal that the single-molecule junction of the 90-mer DNA zipper exhibits high conductance due to the delocalized π system. Moreover, we find an attractive self-restoring capability that the single-molecule junction can be repeatedly formed without full structural breakdown even after electrical failure. The DNA zipping strategy presented here provides a basis for novel designs of single-molecule junctions.

The versatility of DNA has inspired many single-molecule investigations utilizing nanotechnology. Harashima et al. have a somewhat different take on the subject and study a zipper configuration bridging electrodes that resembles an active electro-mechanical component instead.

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.

Multifaceted aspects of charge transfer

Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.

Backbone charge transport in double-stranded DNA

Understanding charge transport in DNA molecules is a long-standing problem of fundamental importance across disciplines^1,2. It is also of great technological interest due to DNA's ability to form versatile and complex programmable structures. Charge transport in DNA-based junctions has been reported using a wide variety of set-ups^2-4, but experiments so far have yielded seemingly contradictory results that range from insulating^5-8 or semiconducting^9,10 to metallic-like behaviour¹¹. As a result, the intrinsic charge transport mechanism in molecular junction set-ups is not well understood, which is mainly due to the lack of techniques to form reproducible and stable contacts with individual long DNA molecules. Here we report charge-transport measurements through single 30-nm-long double-stranded DNA (dsDNA) molecules with an experimental set-up that enables us to address individual molecules repeatedly and to measure the current-voltage characteristics from 5 K up to room temperature. Strikingly, we observed very high currents of tens of nanoamperes, which flowed through both homogeneous and non-homogeneous base-pair sequences. The currents are fairly temperature independent in the range 5-60 K and show a power-law decrease with temperature above 60 K, which is reminiscent of charge transport in organic crystals. Moreover, we show that the presence of even a single discontinuity ('nick') in both strands that compose the dsDNA leads to complete suppression of the current, which suggests that the backbones mediate the long-distance conduction in dsDNA, contrary to the common wisdom in DNA electronics^2-4.

Unique sequence-dependent properties of trinucleotide repeat monolayers: electrochemical, electrical, and topographic characterization

The sequence-dependent properties of the surface-assembled trinucleotide repeat interface on a gold surface were explored by electrochemical methods and surface probe microscopy.

Direct investigation of current transport in cells by conductive atomic force microscopy

Currents play critical roles in neurons. Direct observation of current flows in cells at nanometre dimensions and picoampere current resolution is still a daunting task. In this study, we investigated the current flows in hippocampal neurons, PC12 cells and astrocytes in response to voltages applied to the cell membranes using conductive atomic force microscopy (CAFM). The spines in the hippocampal neurons play crucial roles in nerve signal transfer. When the applied voltage was greater than 7.2 V, PC12 cells even show metallic nanowire-like characteristics. Both the cell body and glial filaments of astrocytes yielded CAFM test results that reflect different electrical conductance. To our best knowledge, the electrical characteristics and current transport through components of cells (especially neurons) in response to an applied external voltage have been revealed for the first time at nanometre dimensions and picoampere current levels. We believe that such studies will pave new ways to study and model the electrical characteristics and physiological behaviours in cells and other biological samples.

Thermal Properties of Ordered and Disordered DNA Chains: Efficient Energy Conversion

Considering the numerous possibilities of having suitable thermoelectric energy conversion at nano-scale level, especially for molecular systems, in the present work we put forward a new proposal along this using a flat DNA segment as a functional element. It is modeled by coupling two chains to a form a two-stranded ladder like geometry, with interactions to first neighbors, within the tight-binding prescription. We critically investigate electrical and thermal properties of DNA molecule depending on the length of the system, temperature, molecule-to-lead coupling and the degree of (correlated) disorder. Our analysis might be helpful in analyzing thermoelectric signatures of correlated and uncorrelated disordered systems, and can be verified in laboratory.

Lab on a tip: Applications of functional atomic force microscopy for the study of electrical properties in biology

Electrical properties, such as charge propagation, dielectrics, surface potentials, conductivity, and piezoelectricity, play crucial roles in biomolecules, biomembranes, cells, tissues, and other biological samples. However, characterizing these electrical properties in delicate biosamples is challenging. Atomic Force Microscopy (AFM), the so called "Lab on a Tip" is a powerful and multifunctional approach to quantitatively study the electrical properties of biological samples at the nanometer level. Herein, the principles, theories, and achievements of various modes of AFM in this area have been reviewed and summarized. STATEMENT OF SIGNIFICANCE: Electrical properties such as dielectric and piezoelectric forces, charge propagation behaviors play important structural and functional roles in biosystems from the single molecule level, to cells and tissues. Atomic force microscopy (AFM) has emerged as an ideal toolkit to study electrical property of biology. Herein, the basic principles of AFM are described. We then discuss the multiple modes of AFM to study the electrical properties of biological samples, including Electrostatic Force Microscopy (EFM), Kelvin Probe Force Microscopy (KPFM), Conductive Atomic Force Microscopy (CAFM), Piezoresponse Force Microscopy (PFM) and Scanning ElectroChemical Microscopy (SECM). Finally, the outlook, prospects, and challenges of the various AFM modes when studying the electrical behaviour of the samples are discussed.

Electron Transfer Methods in Open Systems

Utilization of electron transfer methods for description of quantum transport is popular due to simplicity of the formulation and its ability to account for basic physics of electron exchange between the system and baths. At the same time, the necessity to go beyond simple golden rule-type expressions for rates was indicated in the literature and ad hoc formulations were proposed. Similarly, kinetic schemes for quantum transport beyond the usual second-order Lindblad/Redfield considerations were discussed. Here we utilize recently introduced the nonequilibrium Hubbard Green's function diagrammatic technique to analyze the construction of rates in open systems. We show that previous considerations for rates of second and fourth order can be obtained as a particular case of zero- and second-order Green's function diagrammatic series with bare diagrams. We discuss limitations of previous considerations, stress advantages of the Hubbard Green's function approach in constructing the rates, and indicate that standard dressing of the diagrams is a natural way to account for additional baths/degrees of freedom in the formulation of generalized expressions for the rates.

Advances in Synthesis and Measurement of Charge Transport in DNA-Based Derivatives

Charge transport through molecular structures is interesting both scientifically and technologically. To date, DNA is the only type of polymer that transports significant currents over distances of more than a few nanometers in individual molecules. For molecular electronics, DNA derivatives are by far more promising than native DNA due to their improved charge-transport properties. Here, the synthesis of several unique DNA derivatives along with electrical characterization and theoretical models is surveyed. The derivatives include double stranded poly(G)-poly(C) DNA molecules, four stranded G4-DNA, metal-DNA hybrid molecular wires, and other DNA molecules that are modified either at the bases or at the backbone. The electrical characteristics of these nanostructures, studied experimentally by electrostatic force microscopy, conductive atomic force microscopy, and scanning tunneling microscopy and spectroscopy, are reviewed.

Salt-Induced Assembly Transformation of DNA-AuNP Conjugates Based on RCA Origami: From Linear Arrays to Nanorings

We developed a simple method to adjust the structural transformation of DNA-gold nanoparticles assemblies from linear arrays to nanorings by increasing salt concentrations. A DNA nanoladder constructing from RCA origami acted as templates to assemble periodic AuNPs arrays by a terminal thiol located on staple oligonucleotides. The linear AuNPs arrays could be transformed into nanorings only by changing the concentration of NaCl aqueous solution during the assembly process. It was proven that the electrostatic repulsion, being asymmetrically diminished by the high concentration of NaCl, caused the formation of nanoring architectures.

Single Nanoparticle Magnetic Spin Memristor

There is an increasing demand for the development of a simple Si-based universal memory device at the nanoscale that operates at high frequencies. Spin-electronics (spintronics) can, in principle, increase the efficiency of devices and allow them to operate at high frequencies. A primary challenge for reducing the dimensions of spintronic devices is the requirement for high spin currents. To overcome this problem, a new approach is presented that uses helical chiral molecules exhibiting spin-selective electron transport, which is called the chiral-induced spin selectivity (CISS) effect. Using the CISS effect, the active memory device is miniaturized for the first time from the micrometer scale to 30 nm in size, and this device presents memristor-like nonlinear logic operation at low voltages under ambient conditions and room temperature. A single nanoparticle, along with Au contacts and chiral molecules, is sufficient to function as a memory device. A single ferromagnetic nanoplatelet is used as a fixed hard magnet combined with Au contacts in which the gold contacts act as soft magnets due to the adsorbed chiral molecules.

Effect of interstitial palladium on plasmon-driven charge transfer in nanoparticle dimers

Capacitive plasmon coupling between noble metal nanoparticles (NPs) is characterized by an increasing red-shift of the bonding dipolar plasmon mode (BDP) in the classical electromagnetic coupling regime. This model breaks down at short separations where plasmon-driven charge transfer induces a gap current between the NPs with a magnitude and separation dependence that can be modulated if molecules are present in the gap. Here, we use gap contained DNA as a scaffold for the growth of palladium (Pd) NPs in the gap between two gold NPs and investigate the effect of increasing Pd NP concentration on the BDP mode. Consistent with enhanced plasmon-driven charge transfer, the integration of discrete Pd NPs depolarizes the capacitive BDP mode over longer interparticle separations than is possible in only DNA-linked Au NPs. High Pd NP densities in the gap increases the gap conductance and induces the transition from capacitive to conductive coupling.

Plasmon coupling between nanoparticles may depend not only on interparticle gap distance, but also on gap conductance. Here, the authors modify the gap conductance—and thus the plasmon response—between gold nanoparticle dimers by growing varying amounts of palladium nanoparticles in the gap.

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.

Visualization of periodic electric polarizability of helical nanofibers formed by self-assembly of nucleotide-bearing bolaamphiphiles and natural-source DNA as a template

The possibility of fabricating DNA-based electronics has attracted considerable attention, but constructing robust, functional DNA nanowires on hard substrates has proven to be difficult. This paper describes the production of robust one-dimensional nanofibers by self-assembly of 1,18-nucleotide-bearing bolaamphiphiles templated by salmon sperm DNA. Electrostatic force microscopy measurements of the nanofibers on a highly oriented pyrolytic graphite substrate revealed that they showed electric polarizability that varied periodically with a pitch of 20-30 nm. Atomic force microscopy, gel electrophoresis, and circular dichroism spectroscopy suggested that the periodic polarizability was derived from right-handed helicity induced by the template DNA. Salmon sperm DNA itself did not show electric polarizability.

Multi-dimensional charge transport in supramolecular helical foldamer assemblies

Aromatic foldamers are bioinspired architectures whose potential use in materials remains largely unexplored. Here we report our investigation of vertical and horizontal charge transport over long distances in helical oligo-quinolinecarboxamide foldamers organized as single monolayers on Au or SiO2. Conductive atomic force microscopy showed that vertical conductivity is efficient and that it displays a low attenuation with foldamer length (0.06 Å-1). In contrast, horizontal charge transport is found to be negligible, demonstrating the strong anisotropy of foldamer monolayers. Kinetic Monte Carlo calculations were used to probe the mechanism of charge transport in these helical molecules and revealed the presence of intramolecular through-space charge transfer integrals approaching those found in pentacene and rubrene crystals, in line with experimental results. Kinetic Monte Carlo simulations of charge hopping along the foldamer chain evidence the strong contribution of multiple 1D and 3D pathways in these architectures and their dependence on conformational order. These findings show that helical foldamer architectures may provide a route for achieving charge transport over long distance by combining multiple charge transport pathways.

Formation of Conductive DNA-Based Nanowires via Conjugation of dsDNA with Cationic Peptide

A novel conductive DNA-based nanomaterial, DNA-peptide wire, composed of a DNA core and a peripheral peptide layer, is presented. The electrical conductivity of the wire is found to be at least three orders in magnitude higher than that of native double-stranded DNA (dsDNA). High conductivity of the wires along with a better resistance to mechanical deformations caused by interactions between the substrate and electrode surface make them appealing for a wide variety of nanoelectronic and biosensor applications.

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.

Sequence dependency of the thermodynamic properties of long DNA double-strands

Temperature and sequence dependency of the Pauli paramagnetic susceptibility (PMS) and electronic heat capacity (EHC) of selected configurations are investigated for π-electrons within a ladder model of long DNA double-strands acting as semiconducting nanowires.

Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers

We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of the bases and the hopping parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency [Formula: see text]-550 THz. For dimers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.

Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model

We employ two tight-binding (TB) approaches to systematically study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of N monomers (base pairs): (I) at the base-pair level, using the onsite energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the onsite energies of the bases and the hopping integrals between neighboring bases, i.e., an extended ladder model since we also include diagonal hoppings. We solve a system of M (matrix dimension) coupled equations [(I) M=N, (II) M=2N] for the time-independent problem, and a system of M coupled first order differential equations for the time-dependent problem. We perform a comparative study of stationary and time-dependent aspects of the two TB variants, using realistic sets of parameters. The studied properties include HOMO and LUMO eigenspectra, occupation probabilities, density of states and HOMO-LUMO gaps as well as mean over time probabilities to find the carrier at each site [(I) base pair or (II) base], Fourier spectra, which reflect the frequency content of charge transfer, and pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.

Redox Signaling through DNA

Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

Quantum chemistry and charge transport in biomolecules with superconducting circuits

We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects.

Synthesis and Properties of Novel Silver-Containing DNA Molecules

Migration of silver atoms from silver nano-particles selectively to a double-stranded poly(dG)-poly(dC) polymer leads to metallization of the DNA. As a result the DNA molecules become shorter and thicker (higher), as evident from the atomic force microscopy imaging analysis. The metalized molecules can be detected by transmission and scanning electron microscopy in contrast to the initial non-metalized ones.

Charge transport in a liquid crystalline triphenylene polymer monolayer at air-solid interface

We have prepared a monolayer of a novel liquid crystalline polymer derived from 2,6-dihydroxy-3,7,10,11-tetraalkoxy-triphenylene (PHAT) at an air-water interface and transferred it onto freshly cleaved mica as well as gold coated mica substrates by the Langmuir-Blodgett (L-B) technique. The atomic force microscope (AFM) images of these L-B films show a uniform coverage with a thickness of 1.5 nm. Electrical conductivity measurements were carried out on the PHAT monolayer deposited on the gold coated mica substrate using a current sensing AFM (CSAFM). The gold substrate-PHAT monolayer-cantilever tip of CSAFM forms a metal-insulator-metal (M-I-M) junction. The CSAFM yields a non-linear current-voltage (I-V) curve for the M-I-M junction. The analysis of the I-V characteristics of the M-I-M junction indicated that the charge transport in the liquid crystalline polymer monolayer is by the direct tunneling mechanism. The barrier height for the PHAT monolayer was estimated to be 1.22 ± 0.02 eV.

Hole delocalization over adenine tracts in single stranded DNA oligonucleotides

Adiabatic ionization energies of single stranded DNA oligonucleotides containing adenine tracts of different sizes have been computed at the DFT level and compared with the oxidation potentials determined by differential pulse voltammetry. Geometry optimizations have been performed at the full quantum mechanical level, including the sugar phosphate backbone and solvent effects. The observed progressive lowering of the ionization energy upon increasing the number of consecutive adenines is well predicted, the computed ionization potential shifts being in very good agreement with the experimental outcomes, both by using pure and hybrid functionals. The spin density of the oligonucleotide radical cations is distributed almost over the whole adenine tract, forming delocalized polarons.

Piezoresistivity in single DNA molecules

Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes.

Charge transport and ac response under light illumination in gate-modulated DNA molecular junctions

Using a two-strand tight-binding model and within nonequilibrium Green's function approach, we study charge transport through DNA sequences (GC)NGC and (GC)1(TA)NTA (GC)3 sandwiched between two Pt electrodes. We show that at low temperature DNA sequence (GC)NGC exhibits coherent charge carrier transport at very small bias, since the highest occupied molecular orbital in the GC base pair can be aligned with the Fermi energy of the metallic electrodes by a gate voltage. A weak distance dependent conductance is found in DNA sequence (GC)1(TA)NTA (GC)3 with large NTA. Different from the mechanism of thermally induced hopping of charges proposed by the previous experiments, we find that this phenomenon is dominated by quantum tunnelling through discrete quantum well states in the TA base pairs. In addition, ac response of this DNA junction under light illumination is also investigated. The suppression of ac conductances of the left and right lead of DNA sequences at some particular frequencies is attributed to the excitation of electrons in the DNA to the lead Fermi surface by ac potential, or the excitation of electrons in deep DNA energy levels to partially occupied energy levels in the transport window. Therefore, measuring ac response of DNA junctions can reveal a wealth of information about the intrinsic dynamics of DNA molecules.