Clay Minerals Mediate Folding and Regioselective Interactions of RNA: A Large-Scale Atomistic Simulation Study

Abstract

Since a mineral-mediated origin of life was first hypothesized over 60 years ago, clays have played a significant role in origins of life studies. Such studies have hitherto rarely used computer simulation to understand the possible chemical pathways to the formation of biomolecules. We use molecular dynamics techniques, performed on supercomputing grids, to carry out large-scale simulations of various 25-mer sequences of ribonucleic acid (RNA), in bulk water and with aqueous montmorillonite clay over many tens of nanoseconds. Hitherto, there has only been limited experimental data reported for these systems. Our simulations are found to be in agreement with various experimental observations pertaining to the relative adsorption of RNA on montmorillonite in the presence of charge balancing cations. Over time scales of only a few nanoseconds, specific RNA sequences fold to characteristic secondary structural motifs, which do not form in the corresponding bulk water simulations. Our simulations also show that, in aqueous Ca(2+) environments, RNA can tether to the clay surface through a nucleotide base, leaving the 3'-end of the strand exposed, providing a mechanism for the regiospecific adsorption and elongation of RNA oligomers on clay surfaces.