Molecular dynamics study of the stability of the sarcin/ricin domain of RNA

Abstract

The importance of noncodoing RNAs is being appreciated more. These participate in regulation of all aspects of nucleic acids biology and also have structural and catalytic roles. Noncoding RNAs are assembled from motifs, A‐form helices and unstructured single strands. We are using molecular dynamics (MD) to understand the basis of stability of RNA motifs and their junctions to other motifs and helices.The stability of the sarcin/ricin domain (SRD) RNA motif is being studied in a dumbbell RNA in which a G/C‐rich and a A/U‐rich A‐form helix capped with a tetraloop flank the SRD domain. RNA melting is being observed using adaptively biased and replica exchange methods to explore the free energy profile as the dumbbell melts. We have found that more conformations can be explored more rapidly when the negative charges of the RNA are not completely neutralized by the cations. Artificial cations with less than unit charge allow multiple runs with different degree of neutralization. We are comparing the conformations explored under these conditions with those seen in a standard net neutralized system.