Influence of Surface Chemistry and Charge on Mineral–RNA Interactions

We present the results of large-scale molecular simulations,
run
over several tens of nanoseconds, of 25-mer sequences of single-stranded
ribonucleic acid (RNA) in bulk water and at the surface of three hydrated
positively charged MgAl layered double hydroxide (LDH) minerals. The
three LDHs differ in surface charge density, through varying the number
of isomorphic Al substitutions. Over the course of the simulations,
RNA adsorbs tightly to the LDH surface through electrostatic interactions
between the charged RNA phosphate groups and the alumina charge sites
present in the LDH sheet. The RNA strands arrange parallel to the
surface with the base groups aligning normal to the surface and exposed
to the bulk aqueous region. This templating effect makes LDH a candidate
for amplifying the population of a known RNA sequence from a small
number of RNAs. The structure and interactions of RNA at a positively
charged, hydroxylated LDH surface were compared with those of RNA
at a positively charged calcium montmorillonite surface, allowing
us to establish the comparative effect of complexation and water structure
at hydroxide and silicate surfaces. The systems were studied by computing
radial distribution functions, atom density plots, and radii of gyration,
as well as visualization. An observation pertinent to the role of
these minerals in prebiotic chemistry is that, for a given charge
density on the mineral surface, different genetic sequences of RNA
adopt different configurations.