Solvation and Stabilization of Single-Strand RNA at the Air/Ice Interface Support a Primordial RNA World on Ice

Abstract

Outstanding questions about the RNA world hypothesis for the emergence of life on Earth concern the stability and self-replication of prebiotic aqueous RNA. Recent experimental work has suggested that solid substrates and low temperatures could help resolve these issues. Here, we use classical molecular dynamics simulations to explore the possibility that the substrate is ice itself. We find that at -20 C, a quasi-liquid layer at the air/ice interface solvates a short (8nucleotide) RNA strand such that phosphate groups tend to anchor to specific points of the underlying crystal lattice, lengthening the strand. Hydrophobic bases, meanwhile, tend to migrate to the air/ice interface. Further, contacts between solvent water and ribose 2-OH' groups are found to occur less frequently for RNA on ice than for aqueous RNA at the same temperature; this reduces the likelihood of deprotonation of the 2-OH' and its subsequent nucleophilic attack on the phosphate diester. The implied enhanced resistance to hydrolysis, in turn, could increase opportunities for polymerization and self-copying. These findings thus offer the possibility of a role for an ancient RNA world on ice distinct from that considered in extant elaborations of the RNA world hypothesis. This work is, to the best of our knowledge, the first molecular dynamics study of RNA on ice.

Tuning CO2 Capture at the Gas/Amine Solution Interface by Changing the Solvent Polarity

“…Moreover, Figure b reports an almost barrierless transition between the two gauche conformers, G- and G+, which is in contrast with the barrier of 5 kcal/mol at τ = ∼0° observed at the FPMD level. This difference could be ascribed (a) to the different treatment of the interactions in classical and FPMD, (b) to the limiting sampling in computationally expensive FPMD, and (c) to the optimal choice of methodology for assigning error bars to the free-energy profiles obtained by metadynamics, which is still an open question in the community. − Nevertheless, it is important to mention that the free-energy difference among the minima is comparable between classical and FPMD, implying identical predictions for both classical and FPMD on the relative concentration across conformers in solution. The dynamics along τ is just faster in classical MD than in FPMD, allowing a better sampling of different structures.…”