Statistical Physics of RNA-folding

Abstract

We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large enough costs the model exhibits a thermal denaturation transition which we analyze in terms of the radius of gyration. We point out an inconsistency in the standard approach to RNA secondary structure prediction for large molecules. Under an external force a second order phase transition between a globular and an extended phase takes place. A Harris-type criterion shows that sequence disorder does not affect the correlation length exponent while the other critical exponents are modified in the glass phase. However, at high temperatures, on a coarse-grained level, disordered RNA is well described by a homogeneous model. The characteristics of force-extension curves are discussed as a function of the energy parameters. We show that the force transition is always second order. A re-entrance phenomenon relevant for real disordered RNA is predicted.

accepted for publication in Phys. Rev. E

References in corpus (14)

• Single Molecule Statistics and the Polynucleotide Unzipping Transition
• Dynamical scaling of the DNA unzipping transition
• Statistical mechanics of secondary structures formed by random RNA sequences
• Force-induced denaturation of RNA
• Mechanical denaturation of DNA: existence of a low temperature denaturation
• The secondary structure of RNA under tension
• Nature of the glassy phase of RNA secondary structure
• Tightness of slip-linked polymer chains
• Reversible stretching of homopolymers and random heteropolymers
• Zero Temperature Properties of RNA Secondary Structures
• Mechanical response of random heteropolymers
• Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?
• Reply to the Comment on `Glassy Transition in a Disordered Model for the RNA Secondary Structure'
• Force-induced unfolding of a homopolymer on fractal lattice: exact results vs. mean field predictions

Cited by in corpus (28)

• Single-molecule experiments in biological physics: methods and applications
• Theory for RNA folding, stretching, and melting including loops and salt
• Impact of loop statistics on the thermodynamics of RNA folding
• Statistical mechanics of RNA folding: a lattice approach
• RNA denaturation: excluded volume, pseudoknots and transition scenarios
• Universality class of replica symmetry breaking, scaling behavior, and the low-temperature fixed-point order function of the Sherrington-Kirkpatrick model
• Necklace-Cloverleaf Transition in Associating RNA-like Diblock Copolymers
• Random Euclidean matching problems in one dimension
• Dependence of RNA secondary structure on the energy model
• The Dyck bound in the concave 1-dimensional random assignment model
• Planar diagrams from optimization
• RNA matrix models with external interactions and their asymptotic behaviour
• Thermodynamics of a model for RNA folding
• New alphabet-dependent morphological transition in a random RNA alignment
• Unzipping of two random heteropolymers: Ground state energy and finite size effects
• Unfolding and unzipping of single-stranded DNA by stretching
• RNAlike polymer model: exact calculation on the Bethe lattice
• A model for the force stretching double-stranded chain molecules
• Random RNA under tension
• Interplay between single-stranded binding proteins on RNA secondary structure
• Understanding partonic energy loss from measured light charged particles and jets in PbPb collisions at LHC energies
• Cold denaturation of RNA secondary structures with loop entropy and quenched disorder
• A universality class for RNA-like polymers and double polymers
• A detailed field theory for RNA-like molecules with periodic base sequence
• Working Group Report: Heavy-Ion Physics and Quark-Gluon Plasma
• New phase transition in random planar diagrams and RNA-type matching
• Topological phase transition in a RNA model in the de Gennes regime
• Topological transition in disordered planar matching: combinatorial arcs expansion