Model for Folding and Aggregation in RNA Secondary Structures

Abstract

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the secondary structure and the energy gained by pairing drives the RNA to undergo a “temperature independent” second order phase transition from a molten to an aggregated phase. The aggregated phase thus obtained has a macroscopically large number of contacts between different RNAs. The partition function scaling exponent for this phase is � ≈1/2 and the crossover exponent of the phase transition is � ≈5/3. The relevance of these calculations to the aggregation of biological molecules is discussed.