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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M. Pasi, JH. Maddocks, D. Beveridge, TC. Bishop, DA. Case, T. Cheatham, PD. Dans, B. Jayaram, F. Lankas, C. Laughton, J. Mitchell, R. Osman, M. Orozco, A. Pérez, D. Petkevičiūtė, N. Spackova, J. Sponer, K. Zakrzewska, R. Lavery,
Jazyk angličtina Země Anglie, Velká Británie
Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.
NLK
Directory of Open Access Journals
od 2005
Free Medical Journals
od 1996
PubMed Central
od 1974
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od 1974
Open Access Digital Library
od 1996-01-01 do 2030-12-31
Open Access Digital Library
od 1974-01-01
Open Access Digital Library
od 1996-01-01
Open Access Digital Library
od 1996-01-01
Medline Complete (EBSCOhost)
od 1996-01-01
Oxford Journals Open Access Collection
od 1996-01-01
ROAD: Directory of Open Access Scholarly Resources
od 1974
PubMed
25260586
DOI
10.1093/nar/gku855
Knihovny.cz E-zdroje
- MeSH
- B-DNA chemie MeSH
- konformace nukleové kyseliny MeSH
- párování bází MeSH
- sekvence nukleotidů MeSH
- simulace molekulární dynamiky MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.
Department of Chemistry Indian Institute of Technology Hauz Khas New Delhi 110016 India
Department of Chemistry Wesleyan University Middletown CT 06459 USA
Department of Medicinal Chemistry University of Utah Skaggs 307 Salt Lake City UT 84112 USA
Department of Structural and Chemical Biology Mount Sinai School of Medicine New York NY 10029 USA
Departments of Chemistry and Physics Louisiana Tech University Ruston LA 71270 USA
School of Pharmacy and Centre for Biomolecular Sciences University of Nottingham NG7 2RD UK
Section de Mathématiques Swiss Federal Institute of Technology CH 1015 Lausanne Switzerland
Citace poskytuje Crossref.org
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