Comparison of Models of Thrombin-Binding 15-mer DNA Aptamer by Molecular Dynamics Simulation

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R. V. Reshetnikov^1*, A. V. Golovin¹, and A. M. Kopylov²

¹Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; fax: (495) 939-4195; E-mail: r.reshetnikov@gmail.com

²Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; fax: (495) 939-8846; E-mail: kopylov.alex@gmail.com

^* To whom correspondence should be addressed.

Received December 18, 2009

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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.

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KEY WORDS: aptamer, molecular dynamics simulation, thrombin

DOI: 10.1134/S0006297910080109

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