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

0328589 - ÚOCHB 2010 RIV DE eng J - Journal Article
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. E-ISSN 1521-3765
R&D Projects: GA MŠMT LC512; GA AV ČR IAA400550510; GA ČR GA203/05/0043
Institutional research plan: CEZ:AV0Z40550506
Keywords : DNA structures * solvent effects * stacking interactions
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 5.382, year: 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.
Permanent Link: http://hdl.handle.net/11104/0174878