title: Influence of surface chemistry and charge on mineral-RNA interactions.
abstract: 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.
authors.affiliation: The Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom.
authors.forename: Jacob B
authors.initials: JB
authors.lastname: Swadling
authors.forename: James L
authors.initials: JL
authors.lastname: Suter
authors.forename: H Christopher
authors.initials: HC
authors.lastname: Greenwell
authors.forename: Peter V
authors.initials: PV
authors.lastname: Coveney
mesh_terms: D000535:Aluminum / Q000737:chemistry*; D006878:Hydroxides / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry*; D008903:Minerals / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D012313:RNA / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D006878:Hydroxides; D008903:Minerals; D012313:RNA; D000535:Aluminum; D008274:Magnesium