Molecular Dynamics 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.
Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawińskiego 5a, 02-106 Warsaw, Poland.|Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw , Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland.
Marta
M
Dudek
Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland.
Joanna
http://orcid.org/0000-0002-1464-5323
J
Trylska
D020029:Base Pairing; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D012313:RNA / Q000737:chemistry*; D013237:Stereoisomerism; D014867:Water / Q000737:chemistry
D014867:Water; D012313:RNA