Modelling molecular stability in the RNA world

Abstract

RNA secondary structure, stability and melting curves are calculated for a model of a possible ribozyme corresponding to the RNA directed RNA polymerase (ribopolymerase) required in the RNA world. From these calculations, rates of folding and hybridisation are estimated and used in a stochastic simulation of the dynamics of a population of ribopolymerase molecules. Two models are considered: one synthesising a conventional antiparallel reverse complementary transcript and one synthesising a parallel complementary transcript. It was found that the latter system can operate much more effective in the higher temperatures thought to prevail during the RNA world.