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.