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Multiple Probes are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins

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Changbong Hyeon*^†^‡ and D. Thirumalai*^§;

Center for Theoretical Biological Physics, University of California, San Diego, California 92093, Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea; and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742

J. Am. Chem. Soc., 2008, 130 (5), pp 1538–1539

DOI: 10.1021/ja0771641

Publication Date (Web): January 11, 2008

Section:

General Biochemistry

Abstract

Brownian dynamics simulations, as a function of temperature (T) and force (f) show that RNA hairpins form by multiple pathways thus revealing the rugged nature of the free-energy landscape. While low dimensional free-energy profiles can account for some aspects of thermodynamics of hairpin formation they cannot account for the observed pathway diversity during the refolding process. Thus, a single free-energy surface cannot be used to infer the experimentally observed multistate kinetics in hairpin formation in nucleic acids. The profound differences between the kinetics of folding upon f- and T-quench is due to the slow rate of loop nucleation when the search for the native conformation commences from stretched conformations as is the case upon f-quench.

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