A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

0342528 - ÚOCHB 2011 RIV GB eng J - Journal Article
Lavery, R. - Zakrzewska, K. - Beveridge, D. - Bishop, T. C. - Case, D. A. - Cheatham III, T. E. - Dixit, S. - Jayaram, B. - Lankaš, Filip - Laughton, Ch. - Maddocks, J. H. - Michon, A. - Osman, R. - Orozco, M. - Pérez, A. - Singh, T. - Špačková, Naďa - Šponer, Jiří
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Nucleic Acids Research. Roč. 38, č. 1 (2010), s. 299-313. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA ČR GA203/09/1476; GA MŠMT LC512
Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : B-DNA * molecular dynamics * sequence dependet structure and dynamics
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 7.836, year: 2010

Understanding and predicting base sequence effects on B-DNA properties requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes simulation results providing information not only on all 10 unique base pair steps, but also on all possible neaerst-neighbor effects on these steps. These effects are found to be very significant, impying that dinucleotide models are insufficient for predicting sequence-dependent DNA properties.
Permanent Link: http://hdl.handle.net/11104/0185242