Detailed Information on Publication Record
2014
muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
PASI, Marco, John H. MADDOCKS, David BEVERIDGE, Thomas C. BISHOP, David A. CASE et. al.Basic information
Original name
muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
Authors
PASI, Marco (756 Switzerland), John H. MADDOCKS (756 Switzerland), David BEVERIDGE (826 United Kingdom of Great Britain and Northern Ireland), Thomas C. BISHOP (840 United States of America), David A. CASE (840 United States of America), Thomas CHEATHAM III. (840 United States of America), Pablo D. DANS (724 Spain), B. JAYARAM (356 India), Filip LANKAŠ (203 Czech Republic), Charles LAUGHTON (826 United Kingdom of Great Britain and Northern Ireland), Jonathan MITCHELL (756 Switzerland), Roman OSMAN (840 United States of America), Modesto OROZCO (724 Spain), Alberto PÉREZ (724 Spain), Daiva PETKEVIČIÜTÉ (756 Switzerland), Naďa ŠPAČKOVÁ (203 Czech Republic), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution), Krystyna ZAKRZEWSKA (250 France) and Richard LAVERY (250 France)
Edition
Nucleic Acids Research, Oxford, Oxford University Press, 2014, 0305-1048
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 9.112
RIV identification code
RIV/00216224:14740/14:00077975
Organization unit
Central European Institute of Technology
UT WoS
000347689500044
Keywords in English
BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER
Tags
Tags
International impact, Reviewed
Změněno: 11/3/2015 07:41, Martina Prášilová
Abstract
V originále
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.
Links
ED1.1.00/02.0068, research and development project |
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