Sequence motif dynamics in RNA pools

Abstract

In RNA world scenarios, pools of RNA oligomers form strongly interacting, dynamic systems, which enable molecular evolution. In such pools, RNA oligomers hybridize and dehybridize, ligate and break, ultimately generating longer RNA molecules, which may fold into catalytically active ribozymes. A key process for the elongation of RNA oligomers is templated ligation, which can occur when two RNA strands are adjacently hybridized onto a template strand. Detailed simulations of the dynamics in RNA pools involve a large variety of possible sequences and reactions. Here, we develop a reduced description of these complex dynamics within the space of sequence motifs. We then explore to what extent our reduced description can capture the behavior of detailed simulations that account for the full dynamics in the space of RNA strands. Towards this end, we project the dynamics into a motif space, which accounts only for the abundance of all possible four-nucleotide motifs. A system of ordinary differential equations describes the dynamics of those motifs. Its control parameters are effective rate constants for reactions in motif space, which we obtain from the rate constants for the processes underlying the full dynamics in the space of RNA strands. We find that these reduced motif space dynamics indeed capture important aspects of the informational dynamics of RNA pools in sequence space. This approach could also provide a framework to rationalize and interpret features of the sequence dynamics observed in experimental systems.