Statistical mechanics of RNA folding: a lattice approach

Abstract

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.

arXiv comment8 pages, 9 figures

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Cited by in corpus (10)

• Mesoscopic modeling for nucleic acid chain dynamics
• Universality of collapsing two-dimensional self-avoiding trails
• The Topology of Pseudoknotted Homopolymers
• Anomalous zipping dynamics and forced polymer translocation
• Quantification of the differences between quenched and annealed averaging for RNA secondary structures
• Pseudoknots in a Homopolymer
• Model for Folding and Aggregation in RNA Secondary Structures
• RNAlike polymer model: exact calculation on the Bethe lattice
• Bethe approximation for a DNA-like self-avoiding walk model with variable solvent quality
• Effect of grafting on the binding transition of two flexible polymers