@article{45a4bc48e0814e2a84f86069d248bad2,
title = "μABC: A systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA",
abstract = "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.",
author = "Marco Pasi and Maddocks, {John H.} and David Beveridge and Bishop, {Thomas C.} and Case, {David A.} and Thomas Cheatham and Dans, {Pablo D.} and B. Jayaram and Filip Lankas and Charles Laughton and Jonathan Mitchell and Roman Osman and Modesto Orozco and Alberto P{\'e}rez and Daiva Petkevi{\v c}iute and Nada Spackova and Jiri Sponer and Krystyna Zakrzewska and Richard Lavery",
note = "Funding Information: Swiss National Science Foundation [2000020 143613/1 to J.H.M.]; NSF XSEDE [MCA01S027 to T.E.C.III]; NIH [R-01 GM-081411 to T.E.C.III]; Grant Agency of the Czech Republic [14-21893S to F.L.]; Spanish MINECO [BIO2012-32868 to M.O.]; European Research Council [to M.O.]; ICREA Academia Fellow [to M.O.]; Czech Science Foundation [P208/11/1822 to J.S.]; CEITEC, European Regional Development Fund [CZ.1.05/1.1.00/02.0068 to J.S.]; Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche Project CHROME [ANR-12 BSV5-0017-01 to R.L., K.Z.]. Funding for open access charge: SwissNational Science Foundation [2000020 143613/1]. Publisher Copyright: {\textcopyright} The Author(s) 2014.",
year = "2014",
month = oct,
day = "29",
doi = "10.1093/nar/gku855",
language = "English (US)",
volume = "42",
pages = "12272--12283",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "19",
}