Počet záznamů: 1

Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues

  1. 1.
    0328589 - UOCHB-X 2010 RIV DE eng J - Článek v odborném periodiku
    Zendlová, Lucie - Řeha, D. - Hocek, Michal - Hobza, Pavel
    Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues.
    Chemistry - A European Journal. Roč. 15, č. 31 (2009), s. 7601-7610 ISSN 0947-6539
    Grant CEP: GA MŠk LC512; GA AV ČR IAA400550510; GA ČR GA203/05/0043
    Výzkumný záměr: CEZ:AV0Z40550506
    Klíčová slova: DNA structures * solvent effects * stacking interactions
    Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
    Impakt faktor: 5.382, rok: 2009

    The geometries of a 13 mer of a DNA double helix (5’-GCGTACACATGCG-3’) were determined by molecular dynamics simulations using a Cornell et al. empirical force field. The bases in the central base pair were replaced by a series of hydrophobic base analogues (phenyl, biphenyl, phenylnaphathalene, phenylanthracene and phenylphenanthrene). Due to the large fluctuations of the systems, an average geometry could not be determined. The interaction energies of the Model A, which consisted of three central steps of a duplex without a sugar phosphate backbone, taken from molecular dynamics simulations, were calculated by the selfconsistent charge density functional based tight-binding (SCC-DFTB-D) method and were subsequently averaged. The higher the stability of the systems the higher the aromaticity of the base analogues. To estimate the desolvation energy of the duplex, the COSMO continuum solvent model was used and the calculations were provided on a larger model.
    Trvalý link: http://hdl.handle.net/11104/0174878