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Soft Matter and Biological Physics
Eur. Phys. J. E 9, 67-77 (2002)
DOI: 10.1140/epje/i2002-10057-5

The secondary structure of RNA under tension

M. Müller, F. Krzakala and M. Mézard

Laboratoire de Physique Théorique et Modèles Statistiques, Bât. 100, Université Paris-Sud, F-91405 Orsay, France

muller@ipno.in2p3.fr

(Received 18 June 2002 and Received in final form 23 September 2002 / Published online: 22 November 2002)

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.

PACS
87.14.Gg - DNA, RNA.
87.15.-v - Biomolecules: structure and physical properties.
64.60.-i - General studies of phase transitions.

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2002