Marta Dudek, Joanna Trylska
Centre of New Technologies, University of Warsaw, Poland
M. Dudek, J. Trylska
J. Chem. Theory Comput. 2017, 13:1244-1253, 2017, doi:10.1021/acs.jctc.6b01075
Simulations of L-RNA Involving Homo- and Heterochiral Complexes
L-RNA is a mirror image of the naturally occurring D-RNA. We present the first simulations of L-RNA/D-RNA complexes in the AMBER ff10 force field that we modified to account for L-ribonucleotides. To validate the modifications we performed molecular dynamics simulations of several homo- and heterochiral RNA complexes. We did not observe any canonical base pairing in the L-/D-systems, but we found many repeatable geometric patterns that suggest possible structural motifs between the heterochiral RNA strands. The microscopic picture of L-RNA/D-RNA interface could help formulate the rules for designing L-RNAs with desired affinity toward specific D-RNA motifs.
We provide separate .zip files for AmberTools14 and AmberTools16. Depending which one you plan to use please download appropriate file. For description of the changes made in the parameter files please see Supporting Information of the above article.
The necessary files, descriptions of how the mirror-counterparts of the ribose dihedrals were introduced, and instructions how to use them are also available at https://github.com/martadudek/lrna-amber/
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17 Sep 2012