Hole hopping rates in single strand oligonucleotides

Quantum effects in photosensitization: the case of singlet oxygen generation by thiothymines

Photosensitization is the indirect electronic excitation of a molecule with the aid of a photosensitizer and is a bimolecular nonradiative energy transfer. In this study, we have attempted to elucidate its mechanism, and we do this by calculating rate constants of photosensitization of oxygen by thiothymines (2-thiothymine, 4-thiothymine and 2,4 dithiothymine). The rate constants have been calculated using two approaches: (a) a classical limit of Fermi's Golden Rule (FGR), and (b) a time-dependent variant of FGR, where the treatment is purely quantum mechanical. The former approach has previously been developed for bimolecular systems and has been applied to the photosensitization reactions studied here. The latter approach, however, has so far only been used for unimolecular reactions, and in this work, we describe how it can be adapted for bimolecular reactions. Experimentally, all three thiothymines are known to have significant singlet oxygen yields, which are indicative of similar rates. Rate constants calculated using the time-dependent variant of FGR are similar across all three thiothymines. While the classical approximation gives reasonable rate constants for 2-thiothymine, it severely underestimates them for 4-thiothymine and 2,4 dithiothymine, by several orders of magnitude. This work indicates the importance of quantum effects in driving photosensitization.

Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA

In the framework of a multistep mechanism in which environmental motion triggers comparatively faster elementary electron-transfer steps and stabilizes hole-transfer products, microscopic coherence is crucial for rationalizing the observed yield ratios of oxidative damage to DNA. Interference among probability amplitudes of indistinguishable electron-transfer paths is able to drastically change the final outcome of charge transport, even in DNA oligomers constituted by similar building blocks, and allows for reconciling apparently discordant experimental observations. Properly tailored DNA oligomers appear to be a promising workbench for studying tunneling in the presence of dissipation at the macroscopic level.

The Dynamics of Hole Transfer in DNA

High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.

Single-Stranded DNA Oligonucleotides Retain Rise Coordinates Characteristic of Double Helices

The structures of single-stranded DNA oligonucleotides from dimeric to hexameric sequences have been thoroughly investigated. Computations performed at the density functional level of theory including dispersion forces and solvation show that single-stranded helices adopt conformations very close to crystallographic B-DNA, with rise coordinates amounting up to 3.3 Å. Previous results, suggesting that single strands should be shorter than double helices, largely originated from the incompleteness of the adopted basis set. Although sensible deviations with respect to standard B-DNA are predicted, computations indicate that sequences rich in stacked adenines are the most ordered ones, favoring the B-DNA pattern and inducing regular arrangements also on flanking nucleobases. Several structural properties of double helices rich in adenine are indeed already reflected by the corresponding single strands.

Modeling DNA oxidation in water

A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.

Quantum electron-vibrational dynamics at finite temperature: Thermo field dynamics approach

Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on the thermo field dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. A comparison with the theoretically equivalent density matrix formulation shows the key numerical advantages of the present approach. The solution of thermo field dynamics equations with a novel technique for the propagation of tensor trains (matrix product states) is discussed. Numerical applications to model spin-boson systems show that the present approach is a promising tool for the description of quantum dynamics of complex molecular systems at finite temperature.

Hole delocalization over adenine tracts in single stranded DNA oligonucleotides

Adiabatic ionization energies of single stranded DNA oligonucleotides containing adenine tracts of different sizes have been computed at the DFT level and compared with the oxidation potentials determined by differential pulse voltammetry. Geometry optimizations have been performed at the full quantum mechanical level, including the sugar phosphate backbone and solvent effects. The observed progressive lowering of the ionization energy upon increasing the number of consecutive adenines is well predicted, the computed ionization potential shifts being in very good agreement with the experimental outcomes, both by using pure and hybrid functionals. The spin density of the oligonucleotide radical cations is distributed almost over the whole adenine tract, forming delocalized polarons.

Delocalized hole domains in Guanine-rich DNA oligonucleotides

Differential pulse voltammetries of guanine-rich single- and double-stranded oligonucleotides containing up to six consecutive guanines are reported. The observed progressive lowering of the first voltammetric peak potential as the number of adjacent guanines increases unambiguously points toward the establishment of delocalized hole domains; the hole stabilization energy is ca. 0.1 eV per GG step, significantly lower than that observed for AA steps.

Vibronic couplings and coherent electron transfer in bridged systems

A computational strategy to analyze the dynamics of coherent electron transfer processes in bridged systems, involving three or more electronic states, is presented.