1999
Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer
ŠTEFL, Richard; Eva FADRNÁ a Jaroslav KOČAZákladní údaje
Originální název
Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer
Autoři
ŠTEFL, Richard; Eva FADRNÁ a Jaroslav KOČA
Vydání
Journal of Biomolecular Structure and Dynamics, USA, Adenine Press, 1999, 0739-1102
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10403 Physical chemistry
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Impakt faktor
Impact factor: 1.407
Označené pro přenos do RIV
Ano
Kód RIV
RIV/00216224:14310/99:00000908
Organizační jednotka
Přírodovědecká fakulta
UT WoS
Změněno: 26. 1. 2007 17:26, prof. Mgr. Richard Štefl, Ph.D.
V originále
The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.
Česky
The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.
Návaznosti
| GA203/96/1513, projekt VaV |
| ||
| VS96095, projekt VaV |
|