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Biophys J, September 2001, p. 1324-1332, Vol. 81, No. 3
Department of Physics, University of California at San Diego, La Jolla, California 92093-0319 USA
We quantitatively describe an 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 despite 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 nonequilibrium, 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 an "RNA-pulling server."
Biophys J, September 2001, p. 1324-1332, Vol. 81, No. 3
© 2001 by the Biophysical Society 0006-3495/01/09/1324/09 $2.00
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