Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

0391758 - ÚOCHB 2014 RIV US eng J - Článek v odborném periodiku
Dršata, Tomáš - Pérez, A. - Orozco, M. - Morozov, A. V. - Šponer, Jiří - Lankaš, Filip
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.
Journal of Chemical Theory and Computation. Roč. 9, č. 1 (2013), s. 707-721. ISSN 1549-9618. E-ISSN 1549-9626
Grant CEP: GA ČR(CZ) GAP208/11/1822
Grant ostatní: CEITEC(XE) CZ.1.05/1.1.00/02.0068
Institucionální podpora: RVO:61388963 ; RVO:68081707
Klíčová slova: DNA * mechanical properties * molecular dynamics
Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
Impakt faktor: 5.310, rok: 2013

The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.
Trvalý link: http://hdl.handle.net/11104/0220743