muABC: a systematic microsecond molecular dynamics study of
tetranucleotide sequence effects in B-DNA

J 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:

URL

Impact factor

Impact factor: 9.112

RIV identification code

RIV/00216224:14740/14:00077975

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gku855

UT WoS

000347689500044

Keywords in English

BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER

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

Name: CEITEC - central european institute of technology

Citovat

PASI, Marco, John H. MADDOCKS, David BEVERIDGE, Thomas C. BISHOP, David A. CASE, Thomas CHEATHAM III., Pablo D. DANS, B. JAYARAM, Filip LANKAŠ, Charles LAUGHTON, Jonathan MITCHELL, Roman OSMAN, Modesto OROZCO, Alberto PÉREZ, Daiva PETKEVIČIÜTÉ, Naďa ŠPAČKOVÁ, Jiří ŠPONER, Krystyna ZAKRZEWSKA and Richard LAVERY. muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. Oxford: Oxford University Press, 2014, vol. 42, No 19, p. 12272-12283. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gku855.

@article{1214804,
   author = {Pasi, Marco and Maddocks, John H. and Beveridge, David and Bishop, Thomas C. and Case, David A. and Cheatham III., Thomas and Dans, Pablo D. and Jayaram, B. and Lankaš, Filip and Laughton, Charles and Mitchell, Jonathan and Osman, Roman and Orozco, Modesto and Pérez, Alberto and Petkevičiüté, Daiva and Špačková, Naďa and Šponer, Jiří and Zakrzewska, Krystyna and Lavery, Richard},
   article_location = {Oxford},
   article_number = {19},
   doi = {http://dx.doi.org/10.1093/nar/gku855},
   keywords = {BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA},
   url = {http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full},
   volume = {42},
   year = {2014}
}

TY  - JOUR
ID  - 1214804
AU  - Pasi, Marco - Maddocks, John H. - Beveridge, David - Bishop, Thomas C. - Case, David A. - Cheatham III., Thomas - Dans, Pablo D. - Jayaram, B. - Lankaš, Filip - Laughton, Charles - Mitchell, Jonathan - Osman, Roman - Orozco, Modesto - Pérez, Alberto - Petkevičiüté, Daiva - Špačková, Naďa - Šponer, Jiří - Zakrzewska, Krystyna - Lavery, Richard
PY  - 2014
TI  - muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
JF  - Nucleic Acids Research
VL  - 42
IS  - 19
SP  - 12272-12283
EP  - 12272-12283
PB  - Oxford University Press
SN  - 03051048
KW  - BASE-PAIR
KW  - RECOGNITION
KW  - CONFORMATIONS
KW  - SIMULATIONS
KW  - BACKBONE
KW  - STEPS
KW  - OLIGONUCLEOTIDES
KW  - FLUCTUATIONS
KW  - FLEXIBILITY
KW  - DODECAMER
UR  - http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full
L2  - http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full
N2  - 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.
ER  -

PASI, Marco, John H. MADDOCKS, David BEVERIDGE, Thomas C. BISHOP, David A. CASE, Thomas CHEATHAM III., Pablo D. DANS, B. JAYARAM, Filip LANKAŠ, Charles LAUGHTON, Jonathan MITCHELL, Roman OSMAN, Modesto OROZCO, Alberto PÉREZ, Daiva PETKEVIČIÜTÉ, Naďa ŠPAČKOVÁ, Jiří ŠPONER, Krystyna ZAKRZEWSKA and Richard LAVERY. muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2014, vol.~42, No~19, p.~12272-12283. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gku855.

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