Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2001-01-17
Biophys. J. 81 (2001) 1324-1332
Physics
Condensed Matter
Soft Condensed Matter
final version (with a few minor changes) as will be published in Biophysical Journal
Scientific paper
10.1016/S0006-3495(01)75789-X
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the experimentally-determined free energy rules for RNA secondary structure and models the polymeric properties of the exterior single-stranded regions explicitly as elastic freely-jointed chains. We find that in spite of complicated secondary structures, force-extension curves are typically smooth in quasi-equilibrium. We identify and characterize two sequence/structure-dependent mechanisms that, in addition to the sequence-independent entropic elasticity of the exterior single-stranded regions, are responsible for the smoothness. These involve compensation between different structural elements on which the external force acts simultaneously, and contribution of suboptimal structures, respectively. We estimate how many features a force-extension curve recorded in non-equilibrium, where the pulling proceeds faster than rearrangements in the secondary structure of the molecule, could show in principle. Our software is available to the public through a `RNA-pulling server'.
Bundschuh Ralf
Gerland Ulrich
Hwa Terence
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