Electron Tunneling in DNA

The reorganization energy that accompanies interfacial or through-strand electron tunneling in DNA is remarkably similar to that of a protein, and the attenuation factor for electron transfer between intercalated reagents also remains protein-like. These factors ensure rapid, but short-range electron tunneling through the duplex (shown schematically).     

Watson–Crick Base Pairing Controls Excited‐State Decay in Natural DNA

Excited‐state dynamics are essential to understanding the formation of DNA lesions induced by UV light. By using femtosecond IR spectroscopy, it was possible to determine the lifetimes of the excited states of all four bases in the double‐stranded environment of natural DNA. After UV excitation of the DNA duplex, we detected a concerted decay of base pairs connected by Watson–Crick hydrogen bonds. A comparison of single‐ and double‐stranded DNA showed that the reactive charge‐transfer states formed in the single strands are suppressed by base pairing in the duplex. The strong influence of the Watson–Crick hydrogen bonds indicates that proton transfer opens an efficient decay path in the duplex that prohibits the formation or reduces the lifetime of reactive charge‐transfer states.     

Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime

The positive charge transfer in DNA is investigated, using the first principle treatment of the electron-vibrational interaction. We show that rearrangements of atoms belonging to base pairs induced by charge transfer are essentially quantum mechanical in nature. Particularly at room temperature, around half of the rearrangements occur via quantum tunneling, while the other half takes place via thermally activated transitions. This effect reduces activation energies for charge transfer between both AT and GC pairs by a factor of two compared to their classical values. These behaviors are described within small polaron theory for the non-adiabatic charge transfer and compared to the experimental data and previous theoretical studies.     

Highly selective DNA biosensor based on the long-range electron transfer of indigo carmine through DNA duplex

We have developed a highly selective DNA biosensor. It was based on the long-range electron transfer (LRET) from the electroactive dye indigo carmine (IC) through the DNA duplex on a glassy carbon electrode. Voltammetric experiments showed that IC interacts with dsDNA through a typical intercalative mode with a relatively strong affinity of 2.3(±0.6)?×?10⁶?M^-1. If incubated with DNA in IC solution, no response was observed with the ssDNA-modified probe electrode. However, a pair of well-defined redox peak was observed with a DNA-hybridized electrode, proving the presence of LRET on the biosensor. The biosensor also can differentiate complementary sequences, non-complementary sequences, and even the mutated sequences with single-base mismatches at different sites.

Using atomic layer deposition to hinder solvent decomposition in lithium ion batteries: first-principles modeling and experimental studies

Passivating lithium ion (Li) battery electrode surfaces to prevent electrolyte decomposition is critical for battery operations. Recent work on conformal atomic layer deposition (ALD) coating of anodes and cathodes has shown significant technological promise. ALD further provides well-characterized model platforms for understanding electrolyte decomposition initiated by electron tunneling through a passivating layer. First-principles calculations reveal two regimes of electron transfer to adsorbed ethylene carbonate molecules (EC, a main component of commercial electrolyte), depending on whether the electrode is alumina coated. On bare Li metal electrode surfaces, EC accepts electrons and decomposes within picoseconds. In contrast, constrained density functional theory calculations in an ultrahigh vacuum setting show that, with the oxide coating, e(-) tunneling to the adsorbed EC falls within the nonadiabatic regime. Here the molecular reorganization energy, computed in the harmonic approximation, plays a key role in slowing down electron transfer. Ab initio molecular dynamics simulations conducted at liquid EC electrode interfaces are consistent with the view that reactions and electron transfer occur right at the interface. Microgravimetric measurements demonstrate that the ALD coating decreases electrolyte decomposition and corroborates the theoretical predictions.     

Fully adiabatic dissociative electrochemical electron transfer reactions induced by scanning tunneling microscopy

A theory of fully adiabatic dissociative electrochemical processes of the electron transfer that are induced by scanning tunneling microscopy is constructed. Adiabatic free energy surfaces are calculated and properties of their symmetry are examined under various conditions. Diagrams of kinetic regimes, which characterize possible kinetic processes, which may proceed in the system under consideration, are constructed in the space of model parameters. Dependence of activation free energy on the bias voltage, overvoltage, physical properties of a molecule, and intensity of interaction of a molecule with an electrode and the tip of the scanning tunneling microscope is explored.     

Direct chemical evidence for charge transfer between photoexcited 2-aminopurine and guanine in duplex DNA

Photoexcited 2-aminopurine (Ap*) is extensively exploited as a fluorescent base analogue in the study of DNA structure and dynamics. Quenching of Ap* in DNA is often attributed to stacking interactions between Ap* and DNA bases, despite compelling evidence indicating that charge transfer (CT) between Ap* and DNA bases contributes to quenching. Here we present direct chemical evidence that Ap* undergoes CT with guanine residues in duplex DNA, generating oxidative damage at a distance. Irradiation of Ap in DNA containing the modified guanine, cyclopropylguanosine (CPG), initiates hole transfer from Ap* followed by rapid ring opening of the CPG radical cation. Ring opening accelerates hole trapping to a much shorter time regime than for guanine radicals in DNA; consequently, trapping effectively competes with back electron transfer (BET) leading to permanent CT chemistry. Significantly, BET remains competitive, even with this much faster trapping reaction, consistent with measured kinetics of DNA-mediated CT. The distance dependence of BET is sharper than that of forward CT, leading to an inverted dependence of product yield on distance; at short distances product yield is inhibited by BET, while at longer distances trapping dominates, leading to permanent products. The distance dependence of product yield is distinct from forward CT, or charge injection. As with photoinduced charge transfer in other chemical and biological systems, rapid kinetics for charge injection into DNA need not be associated with a high yield of DNA damage products.     

Selective DNA detection at Zeptomole level based on coulometric measurement of gold nanoparticle-mediated electron transfer across a self-assembled monolayer

A selective DNA sensing with zeptomole detection level is developed based on coulometric measurement of gold nanoparticle (AuNPs)-mediated electron transfer (ET) across a self-assembled monolayer on the gold electrode. After immobilization of a thiolated hairpin-structured DNA probe, an alkanethiol monolayer was self-assembled on the resultant electrode to block [Fe(CN)6 ]-3-/4in a solution from accessing the electrode. In the presence of DNA target, hybridization between the DNA probe and the DNA target breaks the stem duplex of DNA probe. Consequently, stem moiety at the 3′-end of the DNA probes was removed from the electrode surface and made available for hybridization with the reporter DNA-AuNPs conjugates (reporter DNA-AuNPs). The thiolated reporter DNA matches the stem moiety at the 3′-end of the DNA probe. AuNPs were then enlarged by immersing the electrode in a growth solution containing HAuCl 4 and H2O2 after the reporter DNA-AuNPs bound onto the electrode surface. The enlarged AuNPs on the electrode restored the ET between the electrode and the [Fe(CN)6]3 -/4- , as a result, amplified signals were achieved for DNA target detection using the coulometric measurement of Fe(CN)6 3- electro-reduction by prolonging the electrolysis time. The quantities of ET on the DNA sensor increased with the increase in DNA target concentration through a linear range of 3.0 fM to 1.0 pM when electrolysis time was set to 300 s, and the detection limit was 1.0 fM. Correspondingly, thousands of DNA (zeptomole) copies were detected in 10L samples. Furthermore, the DNA sensor showed excellent differentiation ability for single-base mismatch.     

Chemical control of electrode functionalization for detection of DNA hybridization by electrochemical impedance spectroscopy

We report sensitive label-free detection of DNA oligonucleotide sequences using ac impedance measurements. The surface attachment chemistry is critical, and using mixed self-assembled monolayers on a gold electrode results in much better performance than homogeneous self-assembled monolayers. Contrary to expectations, binding of the target sequence reduces rather than increases the charge transfer resistance. Similar behavior is observed on indium tin oxide electrodes, and we ascribe it to the hydrophilicity and rigidity of the DNA duplex that cause it to reside further from the electrode surface and facilitate the approach of negatively charged redox moieties to the interface.     

Recognition of single-base mismatch DNA by Au nanoparticle-assisted electroelution

A simple, convenient and effective method based on the surface plasmon resonance (SPR) technique was introduced for recognition of single-base mismatch DNA (smDNA) by Au nanoparticle (AuNPs)-assisted electroelution. In this method, target DNA, including perfectly matched DNA and smDNA, hybridized with the DNA probes immobilized on Au film and AuNPs, then the Au film was negatively charged. Owing to the difference in stability between single-base mismatch and perfect match DNA, effective distinction between complementary DNA (cDNA) and smDNA was achieved in the presence of an electric field: double-stranded DNA (dsDNA) formed between smDNA targets and DNA probes was denatured by the repulsion force acting on the negatively-charged DNA-linked AuNPs, while the perfectly matched duplex was not influenced. However, if the AuNPs were absent, the effects of cDNA and smDNA were not distinguishable. The effects of electric field intensity and mismatch sites were also investigated. All of the operations were performed under mild conditions. The results showed that AuNP-assisted electroelution may be exploited for the construction of biosensors with high selectivity.     

Mechanistic studies of Fc-PNA(⋅DNA) surface dynamics based on the kinetics of electron-transfer processes

N‐Terminally ferrocenylated and C‐terminally gold‐surface‐grafted peptide nucleic acid (PNA) strands were exploited as unique tools for the electrochemical investigation of the strand dynamics of short PNA(?DNA) duplexes. On the basis of the quantitative analysis of the kinetics and the diffusional characteristics of the electron‐transfer process, a nanoscopic view of the Fc‐PNA(?DNA) surface dynamics was obtained. Loosely packed, surface‐confined Fc‐PNA single strands were found to render the charge‐transfer process of the tethered Fc moiety diffusion‐limited, whereas surfaces modified with Fc‐PNA?DNA duplexes exhibited a charge‐transfer process with characteristics between the two extremes of diffusion and surface limitation. The interplay between the inherent strand elasticity and effects exerted by the electric field are supposed to dictate the probability of a sufficient approach of the Fc head group to the electrode surface, as reflected in the measured values of the electron‐transfer rate constant, k⁰. An in‐depth understanding of the dynamics of surface‐bound PNA and PNA?DNA strands is of utmost importance for the development of DNA biosensors using (Fc‐)PNA recognition layers.     

Sequence‐Dependent Photocurrent Generation through Long‐Distance Excess‐Electron Transfer in DNA

Given its well‐ordered continuous π stacking of nucleobases, DNA has been considered as a biomaterial for charge transfer in biosensors. For cathodic photocurrent generation resulting from hole transfer in DNA, sensitivity to DNA structure and base‐pair stacking has been confirmed. However, such information has not been provided for anodic photocurrent generation resulting from excess‐electron transfer in DNA. In the present study, we measured the anodic photocurrent of a DNA‐modified Au electrode. Our results demonstrate long‐distance excess‐electron transfer in DNA, which is dominated by a hopping mechanism, and the photocurrent generation is sequence dependent.     

Reductive Charge Transfer through an RNA Aptamer

The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non-Watson–Crick base-paired regions might be required. We here demonstrate distance-dependent reductive charge transfer through RNA duplexes and through the non-Watson–Crick base-paired region of an RNA aptamer.     

Long-distance radical cation migration in duplex DNA: the effect of contiguous A.A and T.T mismatches on efficiency and mechanism

A series of DNA oligomers was prepared. Each oligomer contained an anthraquinone group (AQ, sensitizer) covalently linked at a 5'-end and two GG steps that surrounded a variable region. The variable region was composed of A.T base pairs or A.A or T.T mismatches. Irradiation of the AQ injected a radical cation (hole) into the DNA that migrated through the duplex, being trapped by reaction with H2O of O2 at the GG steps. The effect of substituting A.A or T.T mismatches for Watson-Crick base pairs was examined. For A.A mispairs, charge transfer through the mismatch region was as efficient as through normal DNA. For the T.T mismatches, radical cation transport was strongly distance-dependent. These findings suggest that A.A mismatches form a zipper-like motif, and charge transport proceeds by a hopping mechanism. In contrast, charge transport through the T.T mismatches (where there are no purines) may proceed by quantum mechanical tunneling.     

A MutS protein-immobilized au electrode for detecting single-base mismatch of DNA.

A novel electrochemical biosensor was developed to detect gene mutation by using a DNA-mismatch binding protein: MutS from Escherichia coli. The MutS protein was immobilized onto an Au-electrode surface via complex formation between a histidine tag of the MutS protein and a thiol-modified nitrilotriacetic acid chemically adsorbed on the Au-electrode surface. When a target double-stranded DNA having a single-base mismatch was captured by the MutS protein on the electrode, some electrostatic repulsion arose between polyanionic DNA strands and anionic redox couple ions. Consequently, their redox peak currents on a cyclic voltammogram with the Au electrode drastically decreased, depending on the concentration of the target DNA, according to the redox couple-mediated artificial ion-channel principle. By using this assay, one can detect all types of single-base mismatch and single-base deletion.     

First experimental evaluation of partial charge transfer during anion adsorption

The partial charge transfer during anion adsorption cannot be measured in electrochemical experiments or reliably estimated by ab initio quantum-chemical and DFT calculations. However, it is directly involved in the adsorbate charge that is experimentally accessible by in situ contact electric resistance technique. We present the first quantitative evaluation of charge transfer during halides adsorption on silver from aqueous solutions in dependence on the electrode potential. Partial charge transfer from adsorbed bromide and iodide ions to the silver electrode increases with the positive potential shift and may reach complete charge transfer resulting in adatom creation. Chloride adsorption on silver occurs with much lower charge transfer, but on some stainless superalloys it proceeds with substantial charge transfer owing to their specific electronic structure.     

An in situ STM and DTS study of the extremely pure [EMIM]FAP/Au(111) interface

Herein the structure of the interfacial layer between the air- and water-stable ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([EMIM]FAP) and Au(111) is investigated using in situ scanning tunneling microscopy (STM), distance tunneling spectroscopy (DTS) and cyclic voltammetry (CV) measurements. The in situ STM measurements reveal that structured interfacial layers can be probed in both cathodic and anodic regimes at the IL/Au(111) interface. The structure of these layers is dependent on the applied electrode potential, the number of subsequent STM scans and the scan rate. Furthermore, first DTS results show that the tunneling barrier during the 1st STM scan does not seem to change significantly in the cathodic potential regime between the ocp (-0.2 V) and -2.0 V.     

Unmediated by DNA electron transfer in redox-labeled DNA duplexes end-tethered to gold electrodes

Electron transfer (ET) between gold electrodes and redox-labeled DNA duplexes, immobilized onto the electrodes through the alkanethiol linker at the 3'-end and having internal either methylene blue (MB) or anthraquinone (AQ) redox labels, was shown to depend on the redox label charge and the way the redox label is linked to DNA. For loosely packed DNA monolayers, the conjugation of the positively charged MB to DNA through the long and flexible alkane linker provided ET whose kinetics was formally governed by the diffusion of the redox label to the negatively charged electrode surface. For the uncharged AQ label no ET signal was detected. The conjugation of AQ to DNA through the short and more conductive acetylene linker did not provide the anticipated DNA-mediated ET to the AQ-moiety: ET appeared to be low-efficient if any in the studied system, for which no intercalation of AQ within the DNA duplex occurred. The ET communication between the electrode and AQ, built in DNA through the acetylene linker, was achieved only when Ru(NH(3))(6)(3+) molecules were electrostatically attached to the DNA duplex, thus forming the electronic wire. These results are of particular importance both for the fundamental understanding of the interfacial behavior of the redox labeled DNA on electrodes and for the design of biosensors exploiting a variation of ET properties of DNA in the course of hybridization.     

Length‐Independent Charge Transport in Chimeric Molecular Wires

Advanced molecular electronic components remain vital for the next generation of miniaturized integrated circuits. Thus, much research effort has been devoted to the discovery of lossless molecular wires, for which the charge transport rate or conductivity is not attenuated with length in the tunneling regime. Herein, we report the synthesis and electrochemical interrogation of DNA‐like molecular wires. We determine that the rate of electron transfer through these constructs is independent of their length and propose a plausible mechanism to explain our findings. The reported approach holds relevance for the development of high‐performance molecular electronic components and the fundamental study of charge transport phenomena in organic semiconductors.