Comparison of models of thrombin-binding 15-mer DNA aptamer by molecular dynamics simulation

Two models of 15-mer thrombin-binding DNA aptamer (15TGT) were comparatively analyzed by molecular dynamics simulation using the GROMACS software package. The two original models of 15TGT were obtained by NMR and X-ray analyses. The models significantly differ in the topology of loops and the direct...

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Bibliographic Details
Published in:Biochemistry (Moscow) 2010-08, Vol.75 (8), p.1017-1024
Main Authors: Reshetnikov, R. V, Golovin, A. V, Kopylov, A. M
Format: Article
Language:English
Subjects:
Analysis
Aptamers, Nucleotide - chemistry
Aptamers, Nucleotide - metabolism
Biochemistry
Biomedical and Life Sciences
Biomedicine
Bioorganic Chemistry
Chemical properties
Comparative analysis
Computer simulation
Computer-generated environments
Deoxyribonucleic acid
DNA
Life Sciences
Microbiology
Models, Molecular
Molecular Dynamics Simulation
Nucleic Acid Conformation
Thermodynamics
Thrombin
Thrombin - chemistry
Thrombin - metabolism
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Summary:Two models of 15-mer thrombin-binding DNA aptamer (15TGT) were comparatively analyzed by molecular dynamics simulation using the GROMACS software package. The two original models of 15TGT were obtained by NMR and X-ray analyses. The models significantly differ in the topology of loops and the direction of oligodeoxyribonucleotide chain. The evolution of the two structures in parm99 force fields and parmbsc0 optimized for nucleic acids was analyzed in our adaptation of GROMACS architecture. It is shown that the best system for description of the 15TGT structure is the model obtained by X-ray analysis in the parmbsc0 force field.
ISSN:0006-2979
1608-3040
DOI:10.1134/S0006297910080109