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

作者：Pasi Marco; Maddocks John H^*; Beveridge David; Bishop Thomas C; Case David A; Cheatham Thomas III; Dans Pablo D; Jayaram B; Lankas Filip; Laughton Charles; Mitchell Jonathan; Osman Roman; Orozco Modesto; Perez Alberto; Petkeviciute Daiva; Spackova Nada; Sponer Jiri; Zakrzewska Krystyna; Lavery Richard

来源：Nucleic Acids Research, 2014, 42(19): 12272-12283.

DOI：10.1093/nar/gku855

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.

• 出版日期2014-10-29