Modeling DNA oxidation in water

Electron Localization and Mobility in Monolayer Fullerene Networks

The novel 2D quasi-hexagonal phase of covalently bonded fullerene molecules (qHP C60), the so-called graphullerene, has displayed far superior electron mobilities, if compared to the parent van der Waals three-dimensional crystal (vdW C60). Herein, we present a comparative study of the electronic properties of vdW and qHP C60 using state-of-the-art electronic-structure calculations and a full quantum-mechanical treatment of electron transfer. We show that both materials entail polaronic localization of electrons with similar binding energies (≈0.1 eV) and, therefore, they share the same charge transport via polaron hopping. In fact, we quantitatively reproduce the sizable increment of the electron mobility measured for qHP C60 and identify its origin in the increased electronic coupling between C60 units.

Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization

We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.

Salen, salan and salalen zinc(II) complexes in the interaction with HS-: time-resolved fluorescence applications

In the current work we investigate the route of interaction of a newly synthesized family of zinc complexes with HS^- by a plethora of different spectroscopic techniques. A computational analysis on the time dependent density functional theory (TD-DFT) level explored the overall fluorescence properties of the title complexes and their different fluorescence responses to HS^-. Time-resolved fluorescence experiments were also performed and highlight the great potential of the current systems to be implemented as HS^- fluorescent sensors.

Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations

Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.

Theoretical Modeling of Redox Potentials of Biomolecules

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.

The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study

The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800-1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.

Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.

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.

One-electron oxidation of ds(5'-GGG-3') and ds(5'-G(8OG)G-3') and the nature of hole distribution: a density functional theory (DFT) study

Of particular interest in radiation-induced charge transfer processes in DNA is the extent of hole localization immediately after ionization and subsequent relaxation. To address this, we considered double stranded oligomers containing guanine (G) and 8-oxoguanine (8OG), i.e., ds(5'-GGG-3') and ds(5'-G8OGG-3') in B-DNA conformation. Using DFT, we calculated a variety of properties, viz., vertical and adiabatic ionization potentials, spin density distributions in oxidized stacks, solvent and solute reorganization energies and one-electron oxidation potential (E0) in the aqueous phase. Calculations for the vertical state of the -GGG- cation radical showed that the spin was found mainly (67%) on the middle G. However, upon relaxation to the adiabatic -GGG- cation radical, the spin localized (96%) on the 5'-G, as observed in experiments. Hole localizations on the middle G and 3'-G were higher in energy by 0.5 kcal mol-1 and 0.4 kcal mol-1, respectively, than that of 5'-G. In the -G8OGG- cation radical, the spin localized only on the 8OG in both vertical and adiabatic states. The calculated vertical ionization potentials of -GGG- and -G8OGG- stacks were found to be lower than that of the vertical ionization potential of a single G in DNA. The calculated E0 values of -GGG- and -G8OGG- stacks are 1.15 and 0.90 V, respectively, which owing to stacking effects are substantially lower than the corresponding experimental E0 values of their monomers (1.49 and 1.18 V, respectively). SOMO to HOMO level switching is observed in these oxidized stacks. Consequently, our calculations predict that local double oxidations in DNA will form triplet diradical states, which are especially significant for high LET radiations.

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.

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.

Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires

It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) _n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.

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.