Document Detail

Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimer.
MedLine Citation:
PMID:  10333178     Owner:  NLM     Status:  MEDLINE    
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.
R Stefl; E Fadrná; J Koca
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of biomolecular structure & dynamics     Volume:  16     ISSN:  0739-1102     ISO Abbreviation:  J. Biomol. Struct. Dyn.     Publication Date:  1999 Apr 
Date Detail:
Created Date:  1999-08-09     Completed Date:  1999-08-09     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8404176     Medline TA:  J Biomol Struct Dyn     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  1087-95     Citation Subset:  IM    
Department of Organic Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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MeSH Terms
Computer Simulation
DNA, Single-Stranded / chemistry*
Models, Molecular
Nucleic Acid Conformation
Nucleotides / chemistry*
Time Factors
Reg. No./Substance:
0/DNA, Single-Stranded; 0/Nucleotides

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