[Methods of computer modeling and conformational mobility of DNA duplexes].
The review is focused on issues of transferability of the context-sensitive conformational characteristics of DNA estimated from crystallographic structural data on the DNA in aqueous solution. The state of the art in molecular dynamics of charged biopolymers in aqueous solution is covered. Elaboration of expedient force fields and algorithms of calculating long-range electrostatic interactions and solving combined equations of atomic motion have made it possible to generate stable nanosecond trajectories of thermal atomic motion of the biopolymer in aqueous solution in the presence of counterions and salt ions over reasonable time. Tools for analyzing the atomic statistical trajectories of DNA duplexes in aqueous solution to infer context-sensitive conformational dynamic characteristics are discussed together with advances in simulating the mechanisms of global axial bend in DNA duplexes. These techniques allow one to consecutively analyze relationships between the contextual composition of the duplex and the basic modes of essential motions, their amplitude and extent of fluctuation. Development of satisfactory methods for estimating the free energy of biopolymer conformations in solution permits qualitative assessment of the conformational thermodynamic stability of biopolymers and their complexes.
Novosibirsk Institute of Bioorganic Chemistry, Siberian Division, Russian Academy of Sciences, Novosibirsk, 630090 Russia. ynvorob@niboch.nsc.ru
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D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D019563:Mechanics; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry; D055672:Static Electricity
D009692:Nucleic Acid Heteroduplexes; D012333:RNA, Messenger; D004247:DNA