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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F09%3A00328589" target="_blank" >RIV/61388963:_____/09:00328589 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

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

Original language description

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 stabilityof 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.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2009

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Chemistry - A European Journal

ISSN

0947-6539

e-ISSN

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Volume of the periodical

15

Issue of the periodical within the volume

31

Country of publishing house

DE - GERMANY

Number of pages

10

Pages from-to

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UT code for WoS article

000268845000013

EID of the result in the Scopus database

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