Title
Determination of thermodynamics and kinetics of RNA reactions by force
Date Issued
01 November 2006
Access level
open access
Resource Type
review
Author(s)
Universidad de California
Publisher(s)
Cambridge University Press
Abstract
Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force. © 2006 Cambridge University Press.
Start page
325
End page
360
Volume
39
Issue
4
Language
English
OCDE Knowledge area
Termodinámica Biofísica
Scopus EID
2-s2.0-33845681159
PubMed ID
Source
Quarterly Reviews of Biophysics
ISSN of the container
14698994
Sponsor(s)
National Institute of General Medical Sciences R01GM010840
Sources of information: Directorio de Producción Científica Scopus