Nanoscale charge transfer in redox proteins and DNA: Towards biomolecular electronics

Shallow conductance decay along the heme array of a single tetraheme protein wire

Multiheme cytochromes (MHCs) are the building blocks of highly conductive micrometre-long supramolecular wires found in so-called electrical bacteria. Recent studies have revealed that these proteins possess a long supramolecular array of closely packed heme cofactors along the main molecular axis alternating between perpendicular and stacking configurations (TST = T-shaped, stacked, T-shaped). While TST arrays have been identified as the likely electron conduit, the mechanisms of outstanding long-range charge transport observed in these structures remain unknown. Here we study charge transport on individual small tetraheme cytochromes (STCs) containing a single TST heme array. Individual STCs are trapped in a controllable nanoscale tunnelling gap. By modulating the tunnelling gap separation, we are able to selectively probe four different electron pathways involving 1, 2, 3 and 4 heme cofactors, respectively, leading to the determination of the electron tunnelling decay constant along the TST heme motif. Conductance calculations of selected single-STC junctions are in excellent agreement with experiments and suggest a mechanism of electron tunnelling with shallow length decay constant through an individual STC. These results demonstrate that an individual TST motif supporting electron tunnelling might contribute to a tunnelling-assisted charge transport diffusion mechanism in larger TST associations.

RNA BioMolecular Electronics: towards new tools for biophysics and biomedicine

The last half-century has witnessed the birth and development of a new multidisciplinary field at the edge between materials science, nanoscience, engineering, and chemistry known as Molecular Electronics. This field deals with the electronic properties of individual molecules and their integration as active components in electronic circuits and has also been applied to biomolecules, leading to BioMolecular Electronics and opening new perspectives for single-molecule biophysics and biomedicine. Herein, we provide a brief introduction and overview of the BioMolecular electronics field, focusing on nucleic acids and potential applications for these measurements. In particular, we review the recent demonstration of the first single-molecule electrical detection of a biologically-relevant nucleic acid. We also show how this could be used to study biomolecular interactions and applications in liquid biopsy for early cancer detection, among others. Finally, we discuss future perspectives and challenges in the applications of this fascinating research field.

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.

Understanding the electronic properties of single- and double-stranded DNA

Understanding the charge transfer mechanism through deoxyribonucleic acid (DNA) molecules remains a challenge for numerous theoretical and experimental studies in order to be utilized in nanoelectronic devices. Various methods have attempted to investigate the conductivity of double-stranded (ds-) and single-stranded DNA (ssDNA) molecules. However, different electronic behaviors of these molecules are not clearly understood due to the complexity and lack of accuracy of the methods applied in these studies. In this work however, we demonstrated an electronic method to study the electrical behavior of synthetic ssDNA or dsDNA integrated within printed circuit board (PCB)-based metal (gold)-semiconductor (DNA) Schottky junctions. The results obtained in this work are in agreement with other studies reporting dsDNA as having higher conductivity than ssDNA as observed by us in the range of 4-6μA for the former and 2-3μA for the latter at an applied bias of 3V. Selected solid-state parameters such as turn-on voltage, series resistance, shunt resistance, ideality factor, and saturation current were also calculated for the specifically designed ss- and dsDNA sequences using the thermionic emission model. The results also showed that the highest conductance was observed for dsDNA with guanine and cytosine base pairs, while the lowest conductance was for ssDNA with adenine and thymine bases. We believe the results of this preliminary work involving the gold-DNA Schottky junction may allow the interrogation of DNA charge transfer mechanisms and contribute to better understanding its elusive electronic properties.

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

This review is devoted to tight-binding (TB) modeling of nucleic acid sequences like DNA and RNA. It addresses how various types of order (periodic, quasiperiodic, fractal) or disorder (diagonal, non-diagonal, random, methylation et cetera) affect charge transport. We include an introduction to TB and a discussion of its various submodels [wire, ladder, extended ladder, fishbone (wire), fishbone ladder] and of the process of renormalization. We proceed to a discussion of aperiodicity, quasicrystals and the mathematics of aperiodic substitutional sequences: primitive substitutions, Perron–Frobenius eigenvalue, induced substitutions, and Pisot property. We discuss the energy structure of nucleic acid wires, the coupling to the leads, the transmission coefficients and the current–voltage curves. We also summarize efforts aiming to examine the potentiality to utilize the charge transport characteristics of nucleic acids as a tool to probe several diseases or disorders.

Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer

We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of N monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We consider quasi-periodic (Fibonacci, Thue-Morse, Double-Period, Rudin-Shapiro) and fractal (Cantor Set, Asymmetric Cantor Set) polymers made of the same monomer (I polymers) or made of different monomers (D polymers). For all types of such polymers, we calculate the highest occupied molecular orbital (HOMO) eigenspectrum and the lowest unoccupied molecular orbital (LUMO) eigenspectrum, the HOMO-LUMO gap and the density of states. We examine the mean over time probability to find the carrier at each monomer, the frequency content of carrier transfer (Fourier spectra, weighted mean frequency of each monomer, total weighted mean frequency of the polymer), and the pure mean transfer rate k. Our results reveal that there is a correspondence between the degree of structural complexity and the transfer properties. I polymers are more favorable for charge transfer than D polymers. We compare k ( N ) of quasi-periodic and fractal sequences with that of periodic sequences (including homopolymers) as well as with randomly shuffled sequences. Finally, we discuss aspects of experimental results on charge transfer rates in DNA with respect to our coherent pure mean transfer rates.

Exploiting a single intramolecular conformational switching Ni-TPP molecule to probe charge transfer dynamics at the nanoscale on bare Si(100)-2 × 1

Acquiring quantitative information on charge transfer (CT) dynamics at the nanoscale remains an important scientific challenge. In particular, CT processes in single molecules at surfaces need to be investigated to be properly controlled in various devices. To address this issue, the dynamics of switching molecules can be exploited. Here, nickel-tetraphenylporphyrin adsorbed on the Si(100) surface is used to study the CT process ruling the reversible activation of two chiral molecular conformations. Via the electrons of a scanning tunneling microscope (STM), a statistical study of molecular switching reveals two specific locations of the molecule for which their efficiency is optimized. The CT mechanism is shown to propagate from two lateral aryl groups towards the porphyrin macrocycle inducing an intramolecular movement of two symmetric pyrroles. The measured switching efficiencies can thus be related to a Markus-Jordner model to estimate relevant parameters that describe the dynamics of the CT process. Numerical simulations provide a precise description of the molecular conformations and unveil the molecular energy levels that are involved in the CT process. This quantitative method opens a completely original approach to study CT at the nanoscale.

Electronic Properties of Synthetic Shrimp Pathogens-derived DNA Schottky Diodes

The exciting discovery of the semiconducting-like properties of deoxyribonucleic acid (DNA) and its potential applications in molecular genetics and diagnostics in recent times has resulted in a paradigm shift in biophysics research. Recent studies in our laboratory provide a platform towards detecting charge transfer mechanism and understanding the electronic properties of DNA based on the sequence-specific electronic response, which can be applied as an alternative to identify or detect DNA. In this study, we demonstrate a novel method for identification of DNA from different shrimp viruses and bacteria using electronic properties of DNA obtained from both negative and positive bias regions in current-voltage (I–V) profiles. Characteristic electronic properties were calculated and used for quantification and further understanding in the identification process. Aquaculture in shrimp industry is a fast-growing food sector throughout the world. However, shrimp culture in many Asian countries faced a huge economic loss due to disease outbreaks. Scientists have been using specific established methods for detecting shrimp infection, but those methods do have their significant drawbacks due to many inherent factors. As such, we believe that this simple, rapid, sensitive and cost-effective tool can be used for detection and identification of DNA from different shrimp viruses and bacteria.

Vibrational Changes Induced by Electron Transfer in Surface Bound Azurin Metalloprotein Studied by Tip-Enhanced Raman Spectroscopy and Scanning Tunneling Microscopy

The copper protein azurin, due to the peculiar coupling of its optical and vibronic properties with electron transfer (ET) and its biorecognition capabilities, is a very promising candidate for bioelectronic, bio-optoelectronic and biosensor applications. However, a complete understanding of the fundamental processes relating azurin ET and its optical and vibronic characteristics with the charge transport mechanisms occurring in proteins bound to a conductive surface, the typical scenario for a biosensor or bioelectronic component, is still lacking. We studied azurin proteins bound to a gold electrode surface by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy (STM-TERS). Robust TER spectra were obtained, and the protein's vibronic response under optical excitation in resonance with its ligand-to-metal charge transfer band was found to be affected by the tunneling parameters, indicating a direct involvement of the active site vibrations in the electron transport process.

Approaches to single-molecule studies of metalloprotein electron transfer using scanning probe-based techniques

The single-molecule properties of metalloproteins have provided an intensely active research area in recent years. This brief review covers some of the techniques used to prepare, measure and analyse the electron transfer properties of metalloproteins, concentrating on scanning tunnelling microscopy-based techniques and advances in attachment of proteins to electrodes.

Structure, Dynamics, and Electron Transfer of Azurin Bound to a Gold Electrode

Blue copper redox protein azurin (AZ) constitutes an ideal active element for building bionano-optoelectronic devices based on the intriguing interplay among its electron transfer (ET), vibrational, and optical properties. A full comprehension of its dynamical and functional behavior is required for efficient applications. Here, AZ bound to gold electrode via its disulfide bridge was investigated by a molecular dynamics simulation approach taking into account for gold electron polarization which provides a more realistic description of the protein-gold interaction. Upon binding to gold, AZ undergoes slight changes in its secondary structure with the preservation of the copper-containing active site structure. Binding of AZ to gold promotes new collective motions, with respect to free AZ, as evidenced by essential dynamics. Analysis of the ET from the AZ copper ion to the gold substrate, performed by the Pathways model, put into evidence the main residues and structural motifs of AZ involved in the ET paths. During the dynamical evolution of the bionanosystem, transient contacts between some lateral protein atoms and the gold substrate occurred; concomitantly, the opening of additional ET channels with much higher rates was registered. These results provide new and detailed insights on the dynamics and ET properties of the AZ-gold system, by also helping to rationalize some imaging and conductive experimental evidences and also to design new bionanodevices with tailored features.

Differential Electrochemical Conductance Imaging at the Nanoscale

Electron transfer in proteins is essential in crucial biological processes. Although the fundamental aspects of biological electron transfer are well characterized, currently there are no experimental tools to determine the atomic-scale electronic pathways in redox proteins, and thus to fully understand their outstanding efficiency and environmental adaptability. This knowledge is also required to design and optimize biomolecular electronic devices. In order to measure the local conductance of an electrode surface immersed in an electrolyte, this study builds upon the current-potential spectroscopic capacity of electrochemical scanning tunneling microscopy, by adding an alternating current modulation technique. With this setup, spatially resolved, differential electrochemical conductance images under bipotentiostatic control are recorded. Differential electrochemical conductance imaging allows visualizing the reversible oxidation of an iron electrode in borate buffer and individual azurin proteins immobilized on atomically flat gold surfaces. In particular, this method reveals submolecular regions with high conductance within the protein. The direct observation of nanoscale conduction pathways in redox proteins and complexes enables important advances in biochemistry and bionanotechnology.

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.