RNA folding and large N matrix theory

Abstract

We formulate the RNA folding problem as an N× N matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit N→∞ yields the so-called secondary structure (Hartree theory). Tertiary structure and pseudo-knots are obtained by calculating the 1/ N 2 corrections to the partition function. We propose a generalization of the Hartree recursion relation to generate the tertiary structure.