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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F09%3A00328589%21RIV10-MSM-61388963
rdf:type
n5:Vysledek skos:Concept
dcterms: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 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. 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.
dcterms:title
Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues
skos:prefLabel
Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues
skos:notation
RIV/61388963:_____/09:00328589!RIV10-MSM-61388963
n3:aktivita
n12:Z n12:P
n3:aktivity
P(GA203/05/0043), P(IAA400550510), P(LC512), Z(AV0Z40550506)
n3:cisloPeriodika
31
n3:dodaniDat
n13:2010
n3:domaciTvurceVysledku
n4:9496289 n4:2932016 n4:6659160
n3:druhVysledku
n14:J
n3:duvernostUdaju
n8:S
n3:entitaPredkladatele
n17:predkladatel
n3:idSjednocenehoVysledku
346177
n3:idVysledku
RIV/61388963:_____/09:00328589
n3:jazykVysledku
n18:eng
n3:klicovaSlova
DNA structures; solvent effects; stacking interactions
n3:klicoveSlovo
n6:solvent%20effects n6:DNA%20structures n6:stacking%20interactions
n3:kodStatuVydavatele
DE - Spolková republika Německo
n3:kontrolniKodProRIV
[AD45D9534AA3]
n3:nazevZdroje
Chemistry - A European Journal
n3:obor
n16:CF
n3:pocetDomacichTvurcuVysledku
3
n3:pocetTvurcuVysledku
4
n3:projekt
n7:LC512 n7:GA203%2F05%2F0043 n7:IAA400550510
n3:rokUplatneniVysledku
n13:2009
n3:svazekPeriodika
15
n3:tvurceVysledku
Hobza, Pavel Zendlová, Lucie Řeha, D. Hocek, Michal
n3:wos
000268845000013
n3:zamer
n15:AV0Z40550506
s:issn
0947-6539
s:numberOfPages
10