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Biophys. J. BioFAST: First Published February 9, 2007. doi:10.1529/biophysj.106.094243
© 2007 by the Biophysical Society.

A more recent version of this article appeared on May 1, 2007.
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BIOPHYSICAL THEORY AND MODELING

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments

Maria Manosas 1, Jin-Der Wen 2, Pan Li 2, Steve Smith 2, Carlos Bustamante 2, Ignacio Tinoco, Jr. 3* and Felix Ritort 1

1 U. of Barcelona
2 U. of California, Berkeley
3 Univ. of California - Berkeley

* To whom correspondence should be addressed. E-mail: intinoco{at}lbl.gov.

Submitted on July 28, 2006
Revised on September 12, 2006
Accepted on 7 December 2006


  Abstract
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article (1). The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that the longest handles and softest traps that allow detection of the folding/unfolding signal (handles about 5-10 Kbp and traps about 0.03 pN/nm) represent the best conditions to obtain the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules.

Key Words: RNA folding, RNA kinetics, force unfolding, mesoscopic modelling, single molecules




This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
C. Hyeon, G. Morrison, and D. Thirumalai
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
PNAS, July 15, 2008; 105(28): 9604 - 9609.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J.-D. Wen, M. Manosas, P. T. X. Li, S. B. Smith, C. Bustamante, F. Ritort, and I. Tinoco Jr.
Force Unfolding Kinetics of RNA Using Optical Tweezers. I. Effects of Experimental Variables on Measured Results
Biophys. J., May 1, 2007; 92(9): 2996 - 3009.
[Abstract] [Full Text] [PDF]


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Copyright © 2007 by the Biophysical Society.