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Conference publicationsAbstractsXX conferenceEffects of bistability on DNA dynamics in different processes119991, Moscow, Kosygina str., 4, ICP RAN, polymer department 1 pp. (accepted)DNA is one of the most important molecules in nature, therefore it interests very much scientists from different fields - physics, chemistry, biology. However experimental techniques are rather limited and are not always suitable for studying DNA. Many structures , essential for mechanism of such important phenomena as A-B transition, melting, base opening, double helix packing, have very small time range. Also using only experimental methods, it's difficult to get information about energy contribution of different domains of polymer chain and interaction between its parts in physical processes. Therefore computer methods and models are extensively used for investigating DNA. One of the most widely used methods is all-atom molecular dynamics. However, these simulations are rather limited in both time and length scale. Earlier we suggested a coarse-grained model [1,2], which is much more effective that all-atom representation, from computation point of view, but which describes DNA double helix structure, reproduce helical parameters, sound velocity, main features of end-to-end extnsion. However that model is specialized only for small deviations from B-form of DNA, while even in stable B-form inclinations to A-form are observed. In the recent work we analysed all-atom dynamics and enhanced the model by taking into account possibility of conformational transition from B-DNA to A-DNA. For this purpose a two-well potential was introduced, which enabled to take into account existence of two stable conformations of ribose ring. Presence of this mobility allows to adequately simulate dynamics of A-from as well as B-form DNA, what enables to get quantitive agreement of mechanical parameters with experimental values and describe the dynamics of double helix in broad range of physical conditions.
[1] Savin A.V., Mazo M.А., Kikot I.P., Manevitch L.I., Onufriev A. V. Heat conductivity of the DNA double helix // Phys.Rev. B , v. 83, 2011, p. 245406. [2] Kikot I.P., Savin A.V., Zubova E.A., Mazo M.A., Gusarova E.B., Manevitch L.I, Onufriev A.V. New coarse-grained DNA model.// Biophysics, vol. 56, No. 3, 2011, p. 396-402.
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