Literature DB >> 15010932

The secondary structure of RNA under tension.

M Müller1, F Krzakala, M Mézard.   

Abstract

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second-order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a macroscopic end-to-end distance at high forces. At low temperatures, the sequence inhomogeneities modify the critical behaviour. We provide numerical evidence for the universality of the critical exponents which, by extrapolation of the scaling laws to zero force, contain useful information on the ground-state (f = 0) properties. This provides a good method for quantitative studies of scaling exponents characterizing the collapsed globule. In order to get rid of the blurring effect of thermal fluctuations, we restrict ourselves to the ground state at fixed external force. We analyze the statistics of rearrangements, in particular below the critical force, and point out its implications for force-extension experiments on single molecules.

Entities:  

Year:  2002        PMID: 15010932     DOI: 10.1140/epje/i2002-10057-5

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  6 in total

1.  Structural and thermodynamic properties of a linearly perturbed matrix model for RNA folding.

Authors:  I Garg; N Deo
Journal:  Eur Phys J E Soft Matter       Date:  2010-11-18       Impact factor: 1.890

2.  Mechanical unfolding of RNA hairpins.

Authors:  Changbong Hyeon; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-04       Impact factor: 11.205

3.  Forced-unfolding and force-quench refolding of RNA hairpins.

Authors:  Changbong Hyeon; D Thirumalai
Journal:  Biophys J       Date:  2006-02-10       Impact factor: 4.033

4.  Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization.

Authors:  T R Einert; H Orland; R R Netz
Journal:  Eur Phys J E Soft Matter       Date:  2011-06-01       Impact factor: 1.890

5.  Theory for RNA folding, stretching, and melting including loops and salt.

Authors:  Thomas R Einert; Roland R Netz
Journal:  Biophys J       Date:  2011-06-08       Impact factor: 4.033

6.  Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.

Authors:  Jing Qin; Markus Fricke; Manja Marz; Peter F Stadler; Rolf Backofen
Journal:  Algorithms Mol Biol       Date:  2014-09-11       Impact factor: 1.405

  6 in total

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