Polarons and Transport in DNA

Geometrically nonlinear deformation and the emergent behavior of polarons in soft matter

Mechanical strain can alter the electronic structure of both bulk semiconductors as well as nanostructures such as quantum dots. This fact has been extensively researched and exploited for tailoring electronic properties. The strain mediated interaction between the charge carriers and the lattice is interpreted through the so-called deformation potential. In the case of soft materials or nanostructures, such as DNA, the deformation potential leads to the formation of polarons which largely determine the electronic characteristics of DNA and similar polymer entities. In addition, polarons are also speculated to be responsible for the mechanism of quantum actuation in carbon nanotubes. The deformation potential is usually taken to be a linear function of the lattice deformation (U ∼ αε) where α is the deformation potential "constant" that determines the coupling strength and ε is the mechanical strain. In this letter, by carefully accounting for nonlinear geometric deformation that has been hitherto ignored so far in this context, we show that the deformation potential constant is renormalized in a non-trivial manner and is hardly a constant. It varies spatially within the material and with the size of the material. This effect, while negligible for hard materials, is found to be important for soft materials and critically impacts the interpretation of quantities such as polaron size, binding energy, and accordingly, electronic behavior.

A three-step kinetic model for electrochemical charge transfer in the hopping regime

Single-step nonadiabatic electron tunneling models are widely used to analyze electrochemical rates through self-assembled monolayer films (SAMs). For some systems, such as nucleic acids, long-range charge transfer can occur in a "hopping" regime that involves multiple charge transfer events and intermediate states. This report describes a three-step kinetic scheme to model charge transfer in this regime. Some of the features of the three-step model are probed experimentally by changing the chemical composition of the SAM. This work uses the three-step model and a temperature dependence of the charge transfer rate to extract the charge injection barrier for a SAM composed of a 10-mer peptide nucleic acid that operates in the hopping regime.

Study of charge transport mechanisms in (125)I-induced DNA damage at various temperatures

PURPOSE

Iodine-125 decay induces localized DNA damage by three major mechanisms: (1) Direct damage by the emitted Auger electrons, (2) indirect damage by diffusible free radicals, and (3) charge neutralization of the residual, highly positively charged, tellurium daughter atom by stripping electrons from neighboring residues. The charge neutralization mechanism of (125)I-induced DNA damage is poorly understood. Charge transport along a DNA molecules can occur by either a hopping mechanism initiated by charge injection into DNA and propagated by charge migration through DNA bases along the DNA length, or by a tunneling mechanism in which charge transfers directly from a donor to an acceptor residue. In the first case additional damage in DNA nucleotides can be inflicted by the traveling charge; therefore, it is important to learn if charge hopping plays a role in (125)I-decay-induced DNA damage. In our previous work, we determined that at 193K the charge hopping mechanism was not an appreciable component of the mechanism of (125)I-induced DNA damage. However, the question whether this is also the case at higher temperatures remained open.

METHODS

In the current study we used a well-known chemical barrier for charge hopping, 8-oxo-7, 8,-dihydroguanine (8-oxo-G), to assess the role of this mechanism in (125)I-decay-induced DNA damage at the following temperatures: 198, 253, 277 and 298 K.

RESULTS

We found that varying the temperature had little effect on the distribution of (125)I-induced DNA breaks, as well as on the breaks found at the 8-oxo-G probe both with and without piperidine treatment.

CONCLUSIONS

We thus conclude that charge transport by the hopping mechanism is not a major factor in (125)I-decay-induced DNA damage at biologically relevant temperatures.

Analysis of the contribution of charge transport in iodine-125-induced DNA damage

Auger electron emitters like (125)I are the radionuclides of choice for gene-targeted radiotherapy. The highly localized damage they induce in DNA is produced by three mechanisms: direct damage by the emitted Auger electrons, indirect damage by diffusible free radicals produced by Auger electrons traveling in water, and charge neutralization of the residual, highly positively charged tellurium daughter atom by stripping electrons from covalent bonds of neighboring residues. The purpose of our work was to determine whether these mechanisms proceed through an intermediate energy transfer step along DNA. It was proposed that this intermediate step proceeds through the charge transport mechanism in DNA. Conventional charge transport has been described as either a hopping mechanism initiated by charge injection into DNA and propagated by charge migration along the DNA or a tunneling mechanism in which charge moves directly from a donor to an acceptor within DNA. Well-known barriers for the hopping mechanism were used to probe the role of charge transport in (125)I-induced DNA damage. We studied their effect on the distribution of DNA breaks produced by the decay of (125)I in samples frozen at -80 degrees C. We found that these barriers had no measurable effect on the distribution of (125)I-induced breaks.

Trapping and motion of polarons in weakly disordered DNA molecules

Polaron effects for charge migration in DNA molecules have been previously considered within the Peyrard-Bishop-Holstein model. When a uniform electric field is applied, the polaron moves asymptotically at a constant velocity, provided dissipative effects are taken into account, and then current flows through DNA. Disorder originating from interactions with a random environment of solute molecules and ions surrounding the DNA molecule could prevent charge migration due to the localization of the carrier wavefunction. We studied numerically the Peyrard-Bishop-Holstein model when the disordered DNA molecule is subjected to a uniform electric field. We found the threshold value of the electric field to observe polaron motion when disorder is present. We also calculated the fluctuations of the electric current and found that they provide valuable information about the polaron dynamics.

Direct simulation of electron transfer reactions in DNA radical cations

The electron transfer properties of DNA radical cations are important in DNA damage and repair processes. Fast long-range charge transfer has been demonstrated experimentally, but the subtle influences that experimental conditions as well as DNA sequences and geometries have on the details of electron transfer parameters are still poorly understood. In this work, we employ an atomistic QM/MM approach, based on a one-electron tight binding Hamiltonian and a classical molecular mechanics forcefield, to conduct nanosecond length MD simulations of electron holes in DNA oligomers. Multiple spontaneous electron transfer events were observed in 100 ns simulations with neighboring adenine or guanine bases. Marcus parameters of charge transfer could be extracted directly from the simulations. The reorganization energy lambda for hopping between neighboring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1 x 10(9) s(-1) for AA hopping and 1.3 x 10(9) s(-1) for GG hopping were obtained.

Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA

We propose a lattice fermion model suitable for studying the ultrafast photoexcitation dynamics of ordered chains of deoxyribonucleic acid (DNA) polymers. The model includes both parallel (intrachain) and perpendicular (cross-chain) terms as well as diagonal cross-chain terms coupling neighboring bases. The general form of our Hamiltonian is borrowed from lattice fermion models of quantum chromodynamics. The band structure for this model can be determined analytically, and we use this as a basis for computing the singly excited states of the poly(dA)poly(dT) DNA duplex using configuration interaction singles. Parameters for the model are taken from various literature sources and our own ab initio calculations. Results indicate that the excited states consist of a low energy band of dark charge-separated states followed by separate bands of delocalized excitonic states which have weak mixing between the thymidine and adenosine sides of the DNA chain. We then propose a lattice exciton model based upon the transition dipole-dipole couplings between bases and compare the analytical results for the survival probability of an initially localized exciton to exact numerical results. The results herein underscore the competing role of excitonic and charge-transfer dynamics in these systems.

Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.

Charge localization in DNA fibers

We study by first-principles molecular dynamics the mechanism of electron hole (positive charge) localization in a laboratory realizable radical cation Z DNA crystal. We find that at room temperature structural deformation does not provide an efficient localization mechanism. Instead, we find evidence for the importance of changes in the protonation state for stabilizing the radical defect.

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.