Computer simulation of tRNA secondary structure folding

Computer simulation results of folding linear RNA molecules into secondary structures are presented. The structure is formed by two interacting processes: the RNA molecular chain growth (beginning from an initial length, L0), and the structuring (secondary structure sequential growth in the region of the existing molecular chain, based on the local free energy minimization by sequential addition of elementary substructures--stems). It was found that the final secondary structure formation is greatly influenced by the 'structuring period' T (the ratio of the molecular chain growth rate to the structuring rate), and the direction of RNA synthesis. The computer simulation has been performed for 219 and 906 tRNA genes from two published catalogues, on the whole two-dimensional domain (T,L0) parameters, by using four known free-energy models. Minimum stem length and molecular chain growth direction have been also varied. The calculated secondary structures have been compared to the natural tRNA structures given in the catalogues, and the region of best coincidence for the model parameters has been determined. It has been proved that, on average, > 86% of the paired bases of natural tRNA structures appear in the folding simulation.