PHYSICAL JOURNAL E The secondary structure of RNA under tension

Abstract. We study the force-induced unfolding of random disordered RNA or single-stranded DNA poly-mers. 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 uni-versality 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