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. |
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@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.
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