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

SYSNO ASEP	0342528
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
Author(s)	Lavery, R. (FR) Zakrzewska, K. (FR) Beveridge, D. (US) Bishop, T. C. (US) Case, D. A. (US) Cheatham III, T. E. (US) Dixit, S. (CA) Jayaram, B. (IN) Lankaš, Filip (UOCHB-X)_RID Laughton, Ch. (GB) Maddocks, J. H. (CH) Michon, A. (FR) Osman, R. (US) Orozco, M. (ES) Pérez, A. (ES) Singh, T. (IN) Špačková, Naďa (BFU-R)_RID Šponer, Jiří (BFU-R)_{RID, ORCID}
Number of authors	18
Source Title	Nucleic Acids Research. - : Oxford University Press - ISSN 0305-1048 Roč. 38, č. 1 (2010), s. 299-313
Number of pages	15 s.
Language	eng - English
Country	GB - United Kingdom
Keywords	B-DNA ; molecular dynamics ; sequence dependet structure and dynamics
Subject RIV	CF - Physical ; Theoretical Chemistry
R&D Projects	LC06030 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	IAA400040802 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR)
	GA203/09/1476 GA ČR - Czech Science Foundation (CSF)
	LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
	AV0Z50040507 - BFU-R (2005-2011)
	AV0Z50040702 - BFU-R (2007-2013)
UT WOS	000273229100030
DOI	10.1093/nar/gkp834
Annotation	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.
Workplace	Institute of Organic Chemistry and Biochemistry
Contact	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Year of Publishing	2011

Number of the records: 1