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@article{1092256, author = {Dršata, Tomáš and Perez, Alberto and Orozco, Modesto and Morozov, Alexandre V and Šponer, Jiří and Lankaš, Filip}, article_location = {WASHINGTON}, article_number = {1}, doi = {http://dx.doi.org/10.1021/ct300671y}, keywords = {MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION}, language = {eng}, issn = {1549-9618}, journal = {Journal of Chemical Theory and Computation}, title = {Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer}, url = {http://pubs.acs.org/toc/jctcce/9/1}, volume = {9}, year = {2013} }
TY - JOUR ID - 1092256 AU - Dršata, Tomáš - Perez, Alberto - Orozco, Modesto - Morozov, Alexandre V - Šponer, Jiří - Lankaš, Filip PY - 2013 TI - Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer JF - Journal of Chemical Theory and Computation VL - 9 IS - 1 SP - 707-721 EP - 707-721 PB - AMER CHEMICAL SOC SN - 15499618 KW - MOLECULAR-DYNAMICS SIMULATIONS KW - UNIQUE TETRANUCLEOTIDE SEQUENCES KW - NUCLEIC-ACID STRUCTURES KW - B-DNA DODECAMER KW - BASE-PAIR LEVEL KW - X-RAY KW - COUPLING-CONSTANTS KW - MONOVALENT CATIONS KW - CRYSTAL-STRUCTURES KW - ATOMIC-RESOLUTION UR - http://pubs.acs.org/toc/jctcce/9/1 L2 - http://pubs.acs.org/toc/jctcce/9/1 N2 - 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. ER -
DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER and Filip LANKAŠ. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2013, vol.~9, No~1, p.~707-721. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct300671y.
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