Statistical Description of Nucleic Acid Secondary Structure Folding

Abstract

A simple statistical model describing the folding of nucleic acids is proposed. For long sequences the real configuration of the secondary structure is a quasi equilibrium state that cannot be characterised by minimal free energy. This is because the time required to achieve complete thermal equilibrium considerably exceeds the life-time of the molecule. The formation of the secondary structure is represented as a random walk process in the space of all possible molecular configurations. TTie quasi equilibrium structure is obtained by successive linking and disruptions of helix segments with probabilities determined by the rate constants of corresponding unimolecular reactions. The probabilities of configurations consisting of all possible compatible helices are calculated. Structures of some t - RNAs and ribosomal RNAs are analysed.