DYNAMIC COMPETITION BETWEEN ALTERNATIVE STRUCTURES IN VIROID RNAS SIMULATED BY AN RNA FOLDING ALGORITHM

The folding pathways of viroid RNAs were studied using computer simula tions by the genetic algorithm for RNA folding. The folding simulation s were performed for PSTVd RNAs of both polarities, using the wild-typ e sequence and some previously known mutants with suggested changes in the stable or metastable structures. It is shown that metastable mult ihairpin foldings in the minus strand replicative intermediates are es tablished due to the specific folding pathway that ensures the absence of the most stable rod-like structure. Simulations of the PSTVd minus strand folding during transcription reveal a metastable hairpin, form ed in the left terminal domain region of the PSTVd. Despite high seque nce variability, this hairpin is conserved in all known large viroids of both subgroups of PSTVd type, and is presumably necessary to guide the folding of the HPII. hairpin which is functional in the minus stra nd. The folding simulations are able to demonstrate the changes in the balance between metastable and stable structures in mutant PSTVd RNAs . The stable rod-like structure of the circular viroid (+) RNA is also folded via a dynamic folding pathway. Furthermore, the simulations sh ow that intermediate steps iri the forced evolution of a shortened PST Vd replicon may be reconstructed by a mechanistic model of different f olding pathway requirements in plus-and minus-strand RNAs. Thus the fo rmation of viroid RNA structure strongly depends on dynamics of compet ition between alternative RNA structures. This also suggests that the replication efficiency of viroid sequences may be estimated by a simul ation of the folding process. (C) 1998 Academic Press Limited.