High Electronic Conductance through Double-Helix DNA Molecules with Fullerene Anchoring Groups

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.

Colony-Based Electrochemistry Reveals Electron Conduction Mechanisms Mediated by Cytochromes and Flavins in Shewanella oneidensis

Bacteria utilize electron conduction in their communities to drive their metabolism, which has led to the development of various environmental technologies, such as electrochemical microbial systems and anaerobic digestion. It is challenging to measure the conductivity among bacterial cells when they hardly form stable biofilms on electrodes. This makes it difficult to identify the biomolecules involved in electron conduction. In the present study, we aimed to identify c-type cytochromes involved in electron conduction in Shewanella oneidensis MR-1 and examine the molecular mechanisms. We established a colony-based bioelectronic system that quantifies bacterial electrical conductivity, without the need for biofilm formation on electrodes. This system enabled the quantification of the conductivity of gene deletion mutants that scarcely form biofilms on electrodes, demonstrating that c-type cytochromes, MtrC and OmcA, are involved in electron conduction. Furthermore, the use of colonies of gene deletion mutants demonstrated that flavins participate in electron conduction by binding to OmcA, providing insight into the electron conduction pathways at the molecular level. Furthermore, phenazine-based electron transfer in Pseudomonas aeruginosa PAO1 and flavin-based electron transfer in Bacillus subtilis 3610 were confirmed, indicating that this colony-based system can be used for various bacteria, including weak electricigens.

Charge transport properties of ideal and natural DNA segments, as mutation detectors

DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases. A tight-binding (TB) wire model at the base-pair level is recruited, together with a transfer matrix technique. The relevant TB parameters are obtained using a linear combination of all valence orbitals of all atoms, using geometry, either ideal or natural, as the only input. The investigated DNA sequences contain: (i) point substitution mutations - specifically, the transitions guanine (G) ↔ adenine (A) - and (ii) sequences extracted from human chromosomes, modified by expanding the cytosine-adenine-guanine triplet [(CAG)_n repeats] to mimic the following diseases: (a) Huntington's disease, (b) Kennedy's disease, (c) Spinocerebellar ataxia 6, (d) Spinocerebellar ataxia 7. Quantities such as eigenspectra, density of states, transmission coefficients, and the - more experimentally relevant - current-voltage (I-V) curves are studied, intending to find adequate features to recognize mutations. To this end, the normalised deviation of the I-V curve from the origin (NDIV) is also defined. The features of the NDIV seem to provide a clearer picture, being sensitive to the number of point mutations and allowing to characterise the degree of danger of developing the aforementioned diseases.

Learning Conductance: Gaussian Process Regression for Molecular Electronics

Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way toward their routine evaluation.

Conductance and tunnelling current characteristics for individual identification of synthetic nucleic acids with a graphene device

Based on combined density functional theory and non-equilibrium Green's function quantum transport studies, in the present work we have demonstrated the quantum interference (QI) effect on the transverse conductance of Hachimoji (synthetic) nucleic acids when placed between the oxygen-terminated zigzag graphene nanoribbon (O-ZGNR) nanoelectrodes. We theorize that the QI effect could be well preserved in π-π coupling between a target nucleobase molecule and the carbon-based nanoelectrodes. Our study indicates that the QI effect, such as anti-resonance or Fano-resonance, affects the variation of transverse conductance depending on the nucleobase conformation. Furthermore, a variation of up to 2-5 orders of magnitude is observed in the conductance upon rotation for all the nucleobases. The current-voltage (I-V) characteristics results suggest a distinct variation in the electronic tunnelling current across the proposed nanogap device for all five nucleobases with the applied bias voltage ranges from 0.1-1.0 V. The different rotation angles keep the distinct feature of the nucleobases in both transverse conductance and tunnelling current features. Both features could be utilized in an accurate synthetic DNA sequencing device.

Electron ratcheting in self-assembled soft matter

Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations. The first ratcheting mechanism described for nanoscale systems requires local electric fields on the 10⁹ V/m scale to realize nearly 100% population transport. The second ratcheting mechanism for even larger systems, based on electrochemical gating, is estimated to generate currents as large as 0.1 pA for DNA structures that are a few μm in length with a gate voltage of about 5 V, a magnitude comparable to currents measured in DNA wires at the nanoscale when a source-drain voltage bias of similar magnitude is applied, suggesting an approach to considerably extend the distance range over which DNA charge transport devices may operate.

Broadband Dielectric Spectroscopy as a Potential Label-Free Method to Rapidly Verify Ultraviolet-C Radiation Disinfection

Microwave (MW) sensing offers noninvasive, real-time detection of the electromagnetic properties of biological materials via the highly concentrated electromagnetic fields, for which advantages include wide bandwidth, small size, and cost-effective fabrication. In this paper, we present the application of MW broadband dielectric spectroscopy (BDS) coupled to a fabricated biological thin film for evaluating ultraviolet-C (UV-C) exposure effects. The BDS thin film technique could be deployed as a biological indicator for assessing whole-room UV-C surface disinfection. The disinfection process is monitored by BDS as changes in the electrical properties of surface-confined biological thin films photodegraded with UV-C radiation. Fetal bovine serum (FBS, a surrogate for protein) and bacteriophage lambda double-stranded deoxyribonucleic acid (dsDNA) were continuously monitored with BDS during UV-C radiation exposure. The electrical resistance of FBS films yielded promising yet imprecise readings, whereas the resistance of dsDNA films discernibly decreased with UV-C exposure. The observations are consistent with the expected photo-oxidation and photodecomposition of protein and DNA. While further research is needed to characterize these measurements, this study presents the first application of BDS to evaluate the electrical properties of solid-state biological thin films. This technique shows promise toward the development of a test method and a standard biological test to determine the efficacy of UV-C disinfection. Such a test with biological indicators could easily be applied to hospital rooms between patient occupancy for a multipoint evaluation to determine if a room meets a disinfection threshold set for new patients.

Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics

Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.

Selective and easy detection of microcystin-LR in freshwater using a bioactivated sensor based on multiwalled carbon nanotubes on filter paper

Microcystin-LR (MC-LR) is a cyanobacterial toxin produced as a result of eutrophication in polluted water in warm weather conditions. The MC-LR could cause health problems in mammal organs such as the liver, heart, and muscle. Therefore, the World Health Organization (WHO) has stipulated a limit of <1.0 ng/mL in drinking water. Thus, detection and quantification are vital, but current techniques require complex and expensive offsite analysis. We have developed an inexpensive, sensitive, and field-deployable sensor based on bioactivated multiwalled carbon nanotubes (MWCNTs, diameter 20 nm) and micropore filter paper (0.45-μm pore size) for the detection of MC-LR. A specially designed DNA oligonucleotide (5-NH₂-C₆-AN₆) was used as the MC-LR targeting aptamer (MCTA). For bioactivation, MCTA was immobilized on the carboxylated MWCNTs via the formation of amide bonds. The bioactivated MWCNTs were deposited on the micropore filter paper by suction filtering. The detection of MC-LR in freshwater was possible within 1.5 h, achieved by measuring the changes in electrical resistance caused by the selective MC-LR and MCTA interactions. Despite suffering from some matrix effects, the detection limit of the sensor was 0.19 ng/mL for low-concentration MC-LR (≤0.5 ng/mL). This method is much cheaper (biosensor price: < $2.5) than liquid chromatography coupled with tandem mass spectroscopy analysis (ca. $50/sample) which is a standard method for MC-LR detection in a modern laboratory. Thus, this cheap and straightforward MC-LR sensor has applications for detection in remote locations.

From Memristive Materials to Neural Networks

The information technologies have been increasing exponentially following Moore's law over the past decades. This has fundamentally changed the ways of work and life. However, further improving data process efficiency is facing great challenges because of physical and architectural limitations. More powerful computational methodologies are crucial to fulfill the technology gap in the post-Moore's law period. The memristor exhibits promising prospects in information storage, high-performance computing, and artificial intelligence. Since the memristor was theoretically predicted by L. O. Chua in 1971 and experimentally confirmed by HP Laboratories in 2008, it has attracted great attention from worldwide researchers. The intrinsic properties of memristors, such as simple structure, low power consumption, compatibility with the complementary metal oxide-semiconductor (CMOS) process, and dual functionalities of the data storage and computation, demonstrate great prospects in many applications. In this review, we cover the memristor-relevant computing technologies, from basic materials to in-memory computing and future prospects. First, the materials and mechanisms in the memristor are discussed. Then, we present the development of the memristor in the domains of the synapse simulating, in-memory logic computing, deep neural networks (DNNs) and spiking neural networks (SNNs). Finally, the existent technology challenges and outlook of the state-of-art applications are proposed.

Covalent Hyperbranched Polymer Self-Assemblies of Three-Way Junction DNA for Single-Molecule Devices

A hyperbranched polymer (HBP) made of three-way junction (TWJ) DNAs is reported. Three types of 26-mer DNAs with 5'-ends modified with psoralen (PSN) were synthesized. All had self-complementary sequences starting from the 5'-end to the sixth base (AAGCTT), allowing intermolecular hybridization. The base sequences of the remaining 20-mer sites were designed so that upon hybridization, three strands had a TWJ structure with a mass of 25,000 that could be further grown by forming HBPs. PSN photochemically reacts to form interstrand cross-links that increase the polymer stability. Aggregates [(380 ± 44) nm and (65 ± 6) nm] detected with dynamic light scattering for TWJ-DNA solutions were also imaged by electron microscopy and atomic force microscopy, providing evidence of hyperbranched polymerization. The TWJ unit also polymerized on solid substrates such as Au and glass and formed self-assembled monolayers (SAMs). The HBP SAMs were integrated into commercial Pt-interdigitated electrode arrays. The DNA devices had current-voltage curves typical of metal-insulator-metal Schottky diodes; the effective barrier heights and the ideality factors were 0.52 ± 0.002 eV and 21 ± 3.2, respectively. The series resistances were (26 ± 3.3) × 10⁶ Ω, which may provide insights into DNA electron transport. The DNA HBP enables stable electrical connections with probe electrodes and will be an important single-molecule platform.

DNA-Based Fabrication for Nanoelectronics

The bottom-up DNA-templated nanoelectronics exploits the unparalleled self-assembly properties of DNA molecules and their amenability with various types of nanomaterials. In principle, nanoelectronic devices can be bottom-up assembled with near-atomic precision, which compares favorably with well-established top-down fabrication process with nanometer precision. Over the past decade, intensive effort has been made to develop DNA-based nanoassemblies including DNA-metal, DNA-polymer, and DNA-carbon nanotube complexes. This review introduces the history of DNA-based fabrication for nanoelectronics briefly and summarizes the state-of-art advances of DNA-based nanoelectronics. In particular, the most widely applied characterization techniques to explore their unique electronic properties at the nanoscale are described and discussed, including scanning tunneling microscopy, conductive atomic force microscopy, and Kelvin probe force microscopy. We also provide a perspective on potential applications of DNA-based nanoelectronics.

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.

Structure and function of the endothelial surface layer: unraveling the nanoarchitecture of biological surfaces

Among the unsolved mysteries of modern biology is the nature of a lining of blood vessels called the 'endothelial surface layer' or ESL. In venous micro-vessels, it is half a micron in thickness. The ESL is 10 times thicker than the endothelial glycocalyx (eGC) at its base, has been presumed to be comprised mainly of water, yet is rigid enough to exclude red blood cells. How is this possible? Developments in physical chemistry suggest that the venous ESL is actually comprised of nanobubbles of CO2, generated from tissue metabolism, in a foam nucleated in the eGC. For arteries, the ESL is dominated by nanobubbles of O2 and N2 from inspired air. The bubbles of the foam are separated and stabilized by thin layers of serum electrolyte and proteins, and a palisade of charged polymer strands of the eGC. The ESL seems to be a respiratory organ contiguous with the flowing blood, an extension of, and a 'lung' in miniature. This interpretation may have far-reaching consequences for physiology.

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.

Machine Learning Prediction of DNA Charge Transport

First-principles calculations of charge transfer in DNA molecules are computationally expensive given that conducting charge carriers interact with intra- and intermolecular atomic motion. Screening sequences, for example, to identify excellent electrical conductors, is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. We present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3-7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, on-resonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers in the search for promising electronic and thermoelectric materials.

Formulation of Long-Range Transport Rates through Molecular Bridges: From Unfurling to Hopping

Weak fluctuations about the rigid equilibrium structure of ordered molecular bridges drive charge transfer in donor-bridge-acceptor systems via quantum unfurling, which differs from both hopping and ballistic transfer, yet static disorder (low frequency motions) in the bridge is shown to induce a change of mechanism from unfurling to hopping when local fluctuations along the molecular bridge are uncorrelated. Remarkably, these two different transport mechanisms manifest in similar charge-transfer rates, which are nearly independent of the molecular bridge length. We propose an experimental test for distinguishing unfurling from hopping in DNA models with different helix directionality. A unified formulation explains the apparent similarity in the length dependence of the transfer rate despite the difference in the underlying transport mechanisms.