Analytical description of finite size effects for RNA secondary structures

Abstract

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.Comment: 10 pages, 13 figures, published in Phys. Rev.