A partially incoherent rate theory of long-range charge transfer in deoxyribose nucleic acid

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.

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport

We study periodic, quasiperiodic (Thue-Morse, Fibonacci, period doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski, and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A), on the same strand, i.e., our prototype binary alphabet is {G,A}. Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization, and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients, and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.

Manipulation of the magnetoresistance effect in a double-helix DNA

Magnetoresistance (R _m) of a double-stranded (G:C) _N DNA sandwiched between ferromagnetic electrodes has been studied using the transfer matrix method of the tight-binding model. A R _m magnitude up to 72.5% for DNA in its natural structure is observed when the spin-orbit coupling with the helix spring geometry and a possible dephasing effect are taken into account. It can be greatly manipulated by stress or torque applied to the DNA with respect to its axis. In addition, the external voltage bias can also be used to efficiently control R _m. The dependence of R _m on the DNA length in a decaying oscillation form is observed.

Unbiased charge oscillations in B-DNA: monomer polymers and dimer polymers

We call monomer a B-DNA base pair and examine, analytically and numerically, electron or hole oscillations in monomer and dimer polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a N base-pair B-DNA segment. We study highest occupied molecular orbital and lowest unoccupied molecular orbital eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate k to evaluate the easiness of charge transfer. The inverse decay length β for exponential fits k(d), where d is the charge transfer distance, and the exponent η for power-law fits k(N) are computed; generally power-law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of k(d) or k(N) becomes steeper and show the range covered by β and η. Finally, for both the time-independent and the time-dependent problems, we analyze the palindromicity and the degree of eigenspectrum dependence of the probabilities to find the carrier at a particular monomer.

Enhancement of the thermoelectric figure of merit in DNA-like systems induced by Fano and Dicke effects

We report a theoretical study highlighting the thermoelectric properties of biological and synthetic DNA molecules.

EFFECTS OF PHASE-BREAKING ON LONG-RANGE CHARGE TRANSFER IN DNA: PARTIALLY-COHERENT-TUNNELING MODEL STUDY

The mechanism of hole charge transfer in DNA of various lengths and sequences is investigated based on a partially coherent tunneling theory (Zhang et al., J Chem Phys117:4578, 2002), where the effects of phase-breaking in adenine–thymine and guanine–cytosine base pairs are treated on equal foot. This work aims at providing a self-consistent microscopic interpretation for rate experiments on various DNA systems. We will also clarify the condition under which the simple superexchange-mediated-hopping picture is valid, and make some comments on the further development of present theory.

Electronic parameters for charge transfer along DNA

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energies of DNA bases are discussed and then used for calculating the corresponding wave functions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the pi molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons. Our findings are also compared with existing calculations from first principles.

Long-range correlation and charge transfer efficiency in substitutional sequences of DNA molecules

We address the relation between long-range correlations and coherent charge transfer in substitutional DNA sequences using the transfer matrix approach. The substitutional sequences exhibit long-range correlations and show good transmittivity in comparison with uncorrelated random ones. It is found that the charge transfer efficiency varies for different substitutional sequences and many will present electronic delocalization in the system. Further, the resistivity for substitutional sequences may range from decreasing with the length, length independence, or increasing with the length. The conduction mechanisms of various behaviors observed for these sequences are analyzed.

Interpreting DNA Vibrational Circular Dichroism Spectra Using a Coupling Model from Two-Dimensional Infrared Spectroscopy

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.

Dynamical conductance of model DNA sequences

Using a tight binding model, we have investigated charge transport in model DNA sequences under external ac bias. The numerical results of emittance for several model DNA sequences are found to be well described by an analytical formula, especially when the dynamic response is inductivelike. This formula can be understood from general considerations of scattering matrix theory. The temperature dependence of emittance is also studied numerically within the tight binding model, and dynamic response of the model DNA sequences can change from inductivelike to capacitivelike as temperature is varied.

Analysis of Bridge-Mediated Pathways for Long-Range Charge Transfer Systems

With the density matrix decomposition scheme of the path integral method, an accurate quantitative analysis on bridge-mediated pathways in long-range charge transfer processes is presented. Unlike a donor-bridge-acceptor triad, a long-range charge transfer process with a number of bridges has additional pathways in which charges always migrate through bridges but not necessarily by incoherent nearest-neighbor hopping. By employing the density matrix decomposition and sorting the incoherent nearest-neighbor and the coherent next-nearest-neighbor hopping pathways, respective contributions to the charge transfer are evaluated quantitatively. Numerical results of two series of configurations with varying degrees of coherence within the system have found that, depending on the configuration, the contribution of the coherent pathways other than superexchange pathways is significant. In the presence of the coherence, long-range charge transfer dynamics may be dominated by the through-bridge mechanism that consists of the coherent through-bridge pathways as well as the incoherent nearest-neighbor hopping pathways.

Characteristic length scale of electric transport properties of genomes

A tight-binding model together with a statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation parameter Omega is defined to analyze the relation. For some particular propagation length w max, the transport behaviors of the coding and noncoding sequences are very different and the correlation reaches its maximal value Omega max. w max and Omega max are characteristic values for each species. A possible reason for the difference between the features of transport properties in the coding and noncoding regions is the mechanism of DNA damage repair processes together with natural selection.

Environmental Effect on the Relative Contribution of the Charge-Transfer Mechanisms within a Short DNA Sequence

Time evolution of the charge-transfer site population is studied in a short DNA sequence to determine the type of governing charge-transfer mechanism. The system consists of a 5'-GAGGG-3' nucleobase sequence coupled with a dissipative bath that represents the DNA phosphate backbone and solvents. Relative contribution of transfer mechanisms to the whole charge-transfer process has been obtained using the on-the-fly filtered propagator functional path integral method with the density matrix decomposition. Partial density matrixes of the incoherent hopping and coherent superexchange pathways as well as the full reduced density matrix have been evaluated and discussed for both debye and ohmic baths. It was found that the relative contribution of the transfer mechanisms is rather sensitive to the frequency-dependent environmental description.

Static and dynamic aspects of DNA charge transfer: a theoretical perspective

In this work, we approach the impact of dynamic and static disorder on DNA charge transfer from a theoretical and numerical perspective. Disordered or defect geometries are either realized via molecular dynamics simulations using a classical force field or by experimentally determined DNA bulge structures. We apply a chemically specific, atomically resolved extended Su-Schrieffer-Heeger model to compute the energy parameters relevant to DNA charge transfer. For both models studied here, the effective donor-acceptor couplings--and hence the charge transfer rates--significantly depend upon the geometry. Dynamic disorder leads to a correlation time in this quantity of the order of 30 fs, and the transfer rates universally exhibit a broad, yet well-defined, exponential distribution. For DNA bulges, the angle characterizing the defect controls the charge transfer efficiency. The results are discussed and extensively compared to experimental findings and other calculations.

Sequence dependent DNA-mediated conduction

We report on coherent charge transport studies in periodic Poly(dG)-Poly(dC) and aperiodic lambda-phage DNA sequences. The extent and efficiency of charge transfer is discussed as a function of sequence dependent energetics, of temperature dependent base-base couplings, and in relation with experiments.