Search

We estimate solvent reorganization energies λsof electron transfer (ET) in DNA stacks between positively charged guanine (acceptor) and neutral guanine (donor), as well as in rhodamine 6G (R6G)−DNA complexes between R6G (acceptor) and neutral guanine (donor) from molecular dynamics simulations that used a polarizable force field in combination with a polarizable water model. We compare results from the polarizable scheme with those from a common nonpolarizable analogue. We also discuss the influence of charge sets, separate contributions of solute and solvent electronic polarizations, and partial contributions of different molecular groups to changes of λsdue to electronic polarization. Independent of donor−acceptor distances, solvent reorganization energies of ET processes in DNA duplexes from a polarizable force field are about 30% smaller than the corresponding results from a nonpolarizable force field. The effective optical dielectric constant ε̃∞= 1.5, extracted from pertinent scaling factors, is also independent of the donor−acceptor separation over a wide range of distances, from 3.4 to 50.0 Å. Reorganization energies calculated with the polarizable force field agree satisfactorily with experimental data for DNA duplexes. Comparison of results for A-DNA and B-DNA forms as well as for the conformational alignment of the dye relative to the duplex in R6G-DNA complexes demonstrates that the conformation of a duplex hardly affects λs. Among these DNA-related systems, the effective parameter ε̃∞is remarkably constant over a broad range of donor−acceptor distances. [ABSTRACT FROM AUTHOR]

The electronic coupling is one of the key parameters governing electron hole transfer along DNA helices. In this study, we established the first comprehensive data base of electronic coupling elements, calculated at the ab initiolevel. The data set comprises allpossible Watson−Crick base pair dimers, both in standard A-DNA and B-DNA geometries. We also quantified the sensitivity of the coupling elements with respect to geometry changes by varying each of the six standard base step parameters, which specify the relative orientation of neighboring base pairs. We compare the couplings in a systematic way by discussing variations in the coupling magnitude due to geometry or nucleotide sequence in the dimer, and we analyze how the structure affects the electronic coupling in terms of general and dimer-specific trends. Furthermore, we studied how the coupling changes when one introduces the chemically modified base 7-deazaguanine in the corresponding base-pair dimers. Finally, on the basis of the calculated coupling elements, we suggest a model duplex with an enhanced capacity for hole transfer. [ABSTRACT FROM AUTHOR]

Locked nucleic acids (LNAs) exhibit a modified sugar fragment that is restrained to the C3‘-endo conformation. LNA-containing duplexes are rather stable and have a more rigid structure than DNA duplexes, with a propensity for A-conformation of the double helix. To gain detailed insight into the local structure of LNA-modified DNA oligomers (as a foundation for subsequent exploration of the electron-transfer capabilities of such modified duplexes), we carried out molecular dynamics simulations on a set of LNA:DNA 9-mer duplexes and analyzed the resulting structures in terms of base step parameters and the conformations of the sugar residues. The perturbation introduced by a single locked nucleotide was found to be fairly localized, extending mostly to the first neighboring base pairs; such duplexes featured a B-type helix. With increasing degree of LNA modification the structure gradually changed; the duplex with one complete LNA strand assumed a typical A-DNA structure. The relative populations of the sugar conformations agreed very well with NMR data, lending credibility to the validity of the computational protocol. [ABSTRACT FROM AUTHOR]