Phases of the secondary structures of RNA sequences

¹ Department of Physics, UC San Diego-La Jolla, CA 92093-0319, USA
² Physics Department, The Ohio State University - Columbus, OH 43210-1106, USA

Received: 5 February 2002
Accepted: 21 June 2002

Abstract

Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in molecular biophysics. A basic theoretical issue concerns the phase behaviour of self-attracting random RNA sequences. By studying a simplified toy model of RNA folding, we show that there are two distinct possible phases for the random RNA below its melting transition —a molten phase in which an exponentially large number of allowed secondary structures have comparable free energies and coexist in thermal equilibrium, and a glass phase in which the equilibrium ensemble is dominated by one or a few structures with much lower free energies.