RNA denaturation: excluded volume, pseudoknots and transition scenarios

Details RNA denaturation: excluded volume, pseudoknots and transition scenarios RNA denaturation: excluded volume, pseudoknots and transition scenarios

2003-03-12

arxiv.org/abs/cond-mat/0303226v1

Phys. Rev Lett. 91, 198102 (2003)

Physics

Condensed Matter

Soft Condensed Matter

4 pages 3 figures

Scientific paper

10.1103/PhysRevLett.91.198102

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

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