title: Comparison of models of thrombin-binding 15-mer DNA aptamer by molecular dynamics simulation.
abstract: 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.
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia. r.reshetnikov@gmail.com
authors.forename: R V
authors.initials: RV
authors.lastname: Reshetnikov
authors.forename: A V
authors.initials: AV
authors.lastname: Golovin
authors.forename: A M
authors.initials: AM
authors.lastname: Kopylov
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013917:Thrombin / Q000737:chemistry / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; C081676:thrombin aptamer; D013917:Thrombin