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Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues
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SYSNO ASEP 0328589 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues Author(s) Zendlová, Lucie (UOCHB-X)
Řeha, D. (GB)
Hocek, Michal (UOCHB-X) RID, ORCID
Hobza, Pavel (UOCHB-X) RID, ORCIDNumber of authors 4 Source Title Chemistry - A European Journal. - : Wiley - ISSN 0947-6539
Roč. 15, č. 31 (2009), s. 7601-7610Number of pages 10 s. Language eng - English Country DE - Germany Keywords DNA structures ; solvent effects ; stacking interactions Subject RIV CF - Physical ; Theoretical Chemistry R&D Projects LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) IAA400550510 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) GA203/05/0043 GA ČR - Czech Science Foundation (CSF) CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000268845000013 DOI 10.1002/chem.200802170 Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Year of Publishing 2010
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