Charge transport through a molecular π-stack: double helical DNA

Electrical conductivity measurement ofλDNA molecules by conductive atomic force microscopy

Conductive atomic force microscopy (C-AFM) is a powerful tool used in the microelectronics analysis by applying a certain bias voltage between the conducting probe and the sample and obtaining the electrical information of sample. In this work, the surface morphological information and current images of the lambda DNA (λDNA) molecules with different distributions were obtained by C-AFM. The 1 and 10 ngμl^-1DNA solutions were dripped onto mica sheets for making randomly distributed DNA and DNA network samples, and another 1 ngμl^-1DNA sample was placed in a DC electric field with a voltage of 2 V before being dried for stretching the DNA sample. The results show that the current flowing through DNA networks was significantly higher than the stretched and random distribution of DNA in the experiment. TheI-Vcurve of DNA networks was obtained by changing the bias voltage of C-AFM from -9 to 9 V. The currents flowing through stretched DNA at different pH values were studied. When the pH was 7, the current was the smallest, and the current was gradually increased as the solution became acidic or alkaline.

DNA Electrochemistry: Charge-Transport Pathways through DNA Films on Gold

Over the past 25 years, collective evidence has demonstrated that the DNA base-pair stack serves as a medium for charge transport chemistry in solution and on DNA-modified gold surfaces. Since this charge transport depends sensitively upon the integrity of the DNA base pair stack, perturbations in base stacking, as may occur with DNA base mismatches, lesions, and protein binding, interrupt DNA charge transport (DNA CT). This sensitivity has led to the development of powerful DNA electrochemical sensors. Given the utility of DNA electrochemistry for sensing and in response to recent literature, we describe critical protocols and characterizations necessary for performing DNA-mediated electrochemistry. We demonstrate DNA electrochemistry with a fully AT DNA sequence using a thiolated preformed DNA duplex and distinguish this DNA-mediated chemistry from that of electrochemistry of largely single-stranded DNA adsorbed to the surface. We also demonstrate the dependence of DNA CT on a fully stacked duplex. An increase in the percentage of mismatches within the DNA monolayer leads to a linear decrease in current flow for a DNA-bound intercalator, where the reaction is DNA-mediated; in contrast, for ruthenium hexammine, which binds electrostatically to DNA and the redox chemistry is not DNA-mediated, there is no effect on current flow with mismatches. We find that, with DNA as a well hybridized duplex, upon assembly, a DNA-mediated pathway facilitates the electron transfer between a well coupled redox probe and the gold surface. Overall, this report highlights critical points to be emphasized when utilizing DNA electrochemistry and offers explanations and controls for analyzing confounding results.

Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson-Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons' dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

Sulfonylation of 1,4-Diazabicyclo[2.2.2]octane: Charge-Transfer Complex Triggered C-N Bond Cleavage

A novel charge-transfer complex triggered sulfonylation of 1,4-diazabicyclo[2.2.2]octane (DABCO) with mild reaction conditions has been developed. The formation of a charge-transfer complex between electron-withdrawing (hetero)aryl sulfonyl chloride and DABCO allows the synthesis of N-ethylated piperazine sulfonamide in good yields. The reaction has a high functional group tolerance. Spectroscopic studies confirmed the charge-transfer complex formation between sulfonyl chlorides and DABCO, which facilitates the C-N bond cleavage of DABCO.

A novel quantitative electrochemical method to monitor DNA double-strand breaks caused by a DNA cleavage agent at a DNA sensor

To date, DNA cleavage, caused by cleavage agents, has been monitored mainly by gel and capillary electrophoresis. However, these techniques are time-consuming, non-quantitative and require gel stains. In this work, a novel, simple and, importantly, a quantitative method for monitoring the DNA nuclease activity of potential anti-cancer drugs, at a DNA electrochemical sensor, is presented. The DNA sensors were prepared using thiol-modified oligonucleotides that self-assembled to create a DNA monolayer at gold electrode surfaces. The quantification of DNA double-strand breaks is based on calculating the DNA surface coverage, before and after exposure to a DNA cleavage agent. The nuclease properties of a model DNA cleavage agent, copper bis-phenanthroline ([Cu^II(phen)₂]²⁺), that can cleave DNA in a Fenton-type reaction, were quantified electrochemically. The DNA surface coverage decreased on average by 21% after subjecting the DNA sensor to a nuclease assay containing [Cu^II(phen)₂]²⁺, a reductant and an oxidant. This percentage indicates that 6 base pairs were cleaved in the nuclease assay from the immobilised 30 base pair strands. The DNA cleavage can be also induced electrochemically in the absence of a chemical reductant. [Cu^II(phen)₂]²⁺ intercalates between DNA base pairs and, on application of a suitable potential, can be reduced to [Cu^I(phen)₂]⁺, with dissolved oxygen acting as the required oxidant. This reduction process is facilitated through DNA strands via long-range electron transfer, resulting in DNA cleavage of 23%. The control measurements for both chemically and electrochemically induced cleavage revealed that DNA strand breaks did not occur under experimental conditions in the absence of [Cu^II(phen)₂]²⁺.

Guanine-oligothiophene conjugates: liquid-crystalline properties, photoconductivities and ion-responsive emission of their nanoscale assemblies

Liquid-crystalline conjugated guanine–oligothiophene derivatives show electron or ambipolar carrier transport properties and ion-induced phase transition accompanied by a luminescence colour change.

We here report the supramolecular self-assembly of hydrogen-bonded motifs for the development of nanostructured materials that exhibit dynamic functions such as stimuli-responsive properties and molecular recognition behaviour. We have designed and synthesised new thermotropic bicontinuous and columnar liquid-crystalline (LC) guanine–oligothiophene conjugates tethered with lipophilic chains, which exhibit ionic, electronic and photoluminescence properties. Their potassium salt complexes self-assemble into thermotropic columnar LC phases. Time-of-flight photoconductivity measurements have revealed that the guanine–oligothiophene conjugates in the LC states possess charge transport abilities with either electron or ambipolar mobility values of 10^–4 to 10^–3 cm² V^–1 s^–1. Furthermore, we have found that the complexation of potassium ions with the guanine motif could lead not only to structural change and thermal stabilization of the LC phases but also to a photoluminescence colour change in the solid states. The strategy presented in this work could lead to the design of new functional LC materials that could potentially be applicable as sensors and electronic devices.

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.

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

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

Electron interaction with a DNA duplex: dCpdC:dGpdG

Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 5' position (dC˙(-)pdC:dGpdG) or at the 3' position (dCpdC˙(-):dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1H˙pdC:dG2-H(-)pdG and dCpdC2H˙:dGpdG1-H(-). These distonic radical anions are found to be approximately 1 to 4 kcal mol(-1) more stable than the normal radical anions. Intra-strand cytosine π→π transition energies are below the electron detachment energy. Inter-strand π→π transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex.

Length-independent transport rates in biomolecules by quantum mechanical unfurling

Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the longer the bridge, the slower the transfer. This can explain weak length-dependence but not a length-independent transfer rate. We show that the rigid molecular structure of a poly-A bridge supports single step transitions from a localized hole state to delocalized states, spread over the entire bridge. Since propagation to the bridge end is a single step process (termed quantum unfurling) the transfer rate becomes independent of the bridge length. This explanation is consistent with experimental results, and emphasizes the importance of structural order in charge transfer through bio-molecular systems.

A device for measuring spin selectivity in electron transfer

A new type of device is presented that allows direct measurement of spin selectivity in charge transfer processes occurring in adsorbed molecules. The new device provides direct information about the nature of the charge being transferred (electrons or holes) and on spin selectivity, if it exists. Here the device is applied for establishing the spin-dependent electron transfer through double-stranded DNA and its variation with the length of the oligomer. The DNA is self-assembled on a silver substrate and is measured under ambient conditions. The device is based on monitoring the electric potential between a ferromagnetic Ni layer and a silver layer, on top of which the DNA is self-assembled. When a dye molecule, attached to the DNA, is photoexcited, a charge transfer between the dye and the silver substrate takes place, resulting in a change in the electric potential between the Ni and the silver. If the charge transfer is spin selective, the electric potential measured depends on the direction of magnetization of the Ni.

Electron interaction with phosphate cytidine oligomer dCpdC: base-centered radical anions and their electronic spectra

Computational chemistry approach was applied to explore the nature of electron attachment to cytosine-rich DNA single strands. An oligomer dinucleoside phosphate deoxycytidylyl-3',5'-deoxycytidine (dCpdC) was selected as a model system for investigations by density functional theory. Electron distribution patterns for the radical anions of dCpdC in aqueous solution were explored. The excess electron may reside on the nucleobase at the 5' position (dC(•-)pdC) or at the 3' position (dCpdC(•-)). From comparison with electron attachment to the cytosine related DNA fragments, the electron affinity for the formation of the cytosine-centered radical anion in DNA is estimated to be around 2.2 eV. Electron attachment to cytosine sites in DNA single strands might cause perturbations of local structural characteristics. Visible absorption spectroscopy may be applied to validate computational results and determine experimentally the existence of the base-centered radical anion. The time-dependent DFT study shows the absorption around 550-600 nm for the cytosine-centered radical anions of DNA oligomers. This indicates that if such species are detected experimentally they would be characterized by a distinctive color.

Structure determined charge transport in single DNA molecule break junctions

Single DNA conductance measurements with increasing MgCl₂concentrations unambiguously revealed two DNA (B and Z) conformations and the B–Z transition process.

The single-molecule conductance and electrochemical electron-transfer rate are related by a power law

This study examines quantitative correlations between molecular conductances and standard electrochemical rate constants for alkanes and peptide nucleic acid (PNA) oligomers as a function of the length, structure, and charge transport mechanism. The experimental data show a power-law relationship between conductances and charge transfer rates within a given class of molecules with the same bridge chemistry, and a lack of correlation when a more diverse group of molecules is compared, in contrast with some theoretical predictions. Surprisingly, the PNA duplexes exhibit the lowest charge-transfer rates and the highest molecular conductances. The nonlinear rate-conductance relationships for structures with the same bridging chemistries are attributed to differences in the charge-mediation characteristics of the molecular bridge, energy barrier shifts and electronic dephasing, in the two different experimental settings.

Kinetics of adsorption of extended ligands on DNA at small fillings

In the present work, the adsorption kinetics of extended ligands on DNA duplexes at small fillings when molecules of DNA duplexes are on the underlayer within diffusion layer has been investigated. Both diffusion of ligands in solution (diffusion stage) and adsorption of ligands (kinetic stage) are taken into consideration at adsorption of ligands on DNA duplexes. Nonlinear system of differential equations describing adsorption of ligands where not only diffusion stage but also kinetic stage is taken into account, is obtained, moreover the equations allow localizing duplexes in arbitrary place within diffusion layer. Numeric solution of the equations makes possible to investigate the filling kinetics of DNA duplexes by ligands depending on parameters controlling adsorption process. It has been shown that depending on relation between adsorption parameters different kinetic regimes of adsorption - kinetic, complex, and diffusion regimes may be realized.

Exploiting the interaction of metal ions and peptide nucleic acids-DNA duplexes for the detection of a single nucleotide mismatch by electrochemical impedance spectroscopy

The interaction of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with DNA-peptide nucleic acid (PNA) films on a gold surface is studied by electrochemical impedance spectroscopy in the presence of [Fe(CN)(6)](3-/4-) as the redox probe. Impedance data were analyzed with the help of a modified Randles' equivalent circuit. Changes in the charge-transfer resistance, R(CT), decreases in the order of Ni(2+) > Co(2+) > Zn(2+) > Mg(2+). We interpret these results in terms of stronger interactions for Ni(2+) with the DNA-PNA film compared to the other metal ions, potentially involving interactions with the nucleobases, presumably with the N7 of purines or the N3 of pyrimidines. On the basis of these observations, Ni(2+) was chosen to probe the detection of a C-T mismatch in 15-mer PNA-DNA films. Using Ni(2+), it is possible to detect a single C-T mismatch. The resulting DeltaR(CT) is larger for the PNA-DNA hybrid compared to that for the identical 15-mer DNA-DNA hybrid.

Efficient electron delocalization mediated by aromatic homoconjugation in 7,7-diphenylnorbornane derivatives

Efficient electron delocalization by aromatic homoconjugated 7,7-diphenylnorbornane (DPN) in alternated homoconjugated-conjugated block copolymers and reference compounds is revealed by photophysical and electrochemical measurements. The synthesis of the polymers was achieved by Suzuki polycondensation reaction. Effective electron delocalization by DPN is demonstrated by the significant red shifts observed in the absorption and emission spectra and the variation of the energy band gap of the polymers and monomeric model compounds in comparison to a series of oligophenylenes used as references (p-quaterphenyl, p-terphenyl, and biphenyl). The electron delocalization is also clearly demonstrated by the lower oxidation potential measured for homoconjugated model compound in comparison to p-terphenyl. The results show that the electron delocalization caused by two homoconjugated aryl rings is comparable to the effect produced by one conjugated aryl ring.

Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.

The role of pyrimidine nucleobase excimers in DNA photophysics and photoreactivity

Quantum chemical studies using the accurate CASPT2//CASSCF procedure show that π-stacked interactions in biochromophores such as pyrimidine (Pyr) DNA/RNA nucleobases pairs yield excimer-like situations which behave as precursors of processes like charge transfer (CT) or photoreactivity and are the source of the emissive properties in DNA. Examples are the CT between adjacent DNA nucleobases in a strand of oligonucleotides and the photodimerization taking place in cytosine (C) pairs leading to cyclobutanecytosine (CBC) mutants. These processes take place through nonadiabatic photochemical mechanisms whose evolution is determined by the presence and accessibility of conical intersections (CIs) and other surface crossings between different electronic states.

Switchable redox activity by proton fuelled DNA nano-machines

The switching electrochemical property of an SWNT/DNA hybrid can be produced through reversible conformational changes between the closed and open state originating from the pH-responding i-motif DNA which significantly improves its molecular switching and stability by hydrophobic interactions with SWNTs.

Detection of single-nucleotide mismatches using scanning electrochemical microscopy

Probing ds-DNA films in the presence of Zn(2+) ions by scanning electrochemical microscopy (SECM) allows the unequivocal detection of a single-nucleotide mismatch and provides information about its position within the duplex.

Genotoxicity of combined exposure to polycyclic aromatic hydrocarbons and UVA--a mechanistic study

Solar UV radiation and benzo[a]pyrene (BaP) are two carcinogenic agents. When combined, their deleterious properties are synergistic. In order to get insights into the underlying processes, we carried out a mechanistic study within isolated DNA photosensitized to UVA radiation by either BaP, its diol epoxide metabolite (BPDE) or the tetraol arising from the hydrolysis of this last molecule. Measurement of the level of the oxidized base 8-oxo-7,8-dihydroguanine revealed that BaP is a poor sensitizer while BPDE and tetraol are more potent ones. None of these compounds was found to photosensitize formation of cyclobutane pyrimidine dimers through triplet energy transfer. On the basis of the distribution of oxidized DNA bases, we could show that photosensitization of DNA by BPDE involves electron abstraction (Type I) while tetraol acts mainly through singlet oxygen production (Type II). Under our experimental conditions, Type I was the major photosensitization process, which shows the lack of involvement of tetraol in the observed photo-oxidation reaction. Finally, we could show that the adducts, resulting from the alkylation of DNA by BPDE, are very potent sensitizers. Indeed, they are located in the close vicinity of the double helix and thus perfectly placed to induce oxidation reactions.

Electronic coupling between base pair dimers of LNA:DNA oligomers

We calculated ab initio electronic coupling elements between neighboring base-pair dimers in a set of LNA:DNA oligomers with different numbers of locked nucleotides and compared them by averaging the values over ensembles of snapshots from molecular dynamics trajectories. Averaging was based on coupling elements for various ensembles comprising of 33,000 structures. The known pronounced variations of coupling elements on the nanosecond timescale due to thermal fluctuations of the DNA structure were confirmed. We found significant differences in electronic coupling at the dimer level between a non-modified DNA:DNA duplex and the corresponding duplex containing one fully LNA-substituted strand. We rationalized these differences by very dissimilar overlap in the pi-stack as a consequence of the LNA-modified system approximating an A-DNA-type helix. The calculated coupling elements for the non-modified reference duplex were similar to those of standard B-DNA and those for the fully modified oligomer resembled the matrix elements estimated for standard A-DNA.