RNA denaturation: excluded volume, pseudoknots and transition scenarios

Abstract

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.

arXiv comment4 pages 3 figures

References in corpus (8)

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Cited by in corpus (6)

• Impact of loop statistics on the thermodynamics of RNA folding
• The Topology of Pseudoknotted Homopolymers
• Quantification of the differences between quenched and annealed averaging for RNA secondary structures
• Model for Folding and Aggregation in RNA Secondary Structures
• Bethe approximation for a DNA-like self-avoiding walk model with variable solvent quality
• RNAlike polymer model: exact calculation on the Bethe lattice