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.

Základní údaje

Originální název

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

Autoři

PASI, Marco (756 Švýcarsko), John H. MADDOCKS (756 Švýcarsko), David BEVERIDGE (826 Velká Británie a Severní Irsko), Thomas C. BISHOP (840 Spojené státy), David A. CASE (840 Spojené státy), Thomas CHEATHAM III. (840 Spojené státy), Pablo D. DANS (724 Španělsko), B. JAYARAM (356 Indie), Filip LANKAŠ (203 Česká republika), Charles LAUGHTON (826 Velká Británie a Severní Irsko), Jonathan MITCHELL (756 Švýcarsko), Roman OSMAN (840 Spojené státy), Modesto OROZCO (724 Španělsko), Alberto PÉREZ (724 Španělsko), Daiva PETKEVIČIÜTÉ (756 Švýcarsko), Naďa ŠPAČKOVÁ (203 Česká republika), Jiří ŠPONER (203 Česká republika, garant, domácí), Krystyna ZAKRZEWSKA (250 Francie) a Richard LAVERY (250 Francie)

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2014, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.112

Kód RIV

RIV/00216224:14740/14:00077975

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000347689500044

Klíčová slova anglicky

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

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 3. 2015 07:41, Martina Prášilová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: 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 a Richard LAVERY. muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. Oxford: Oxford University Press, 2014, roč. 42, č. 19, s. 12272-12283. ISSN 0305-1048. Dostupné z: 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 a 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, roč.~42, č.~19, s.~12272-12283. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku855.

Podrobný výpis o publikaci