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Structures, Kinetics, Thermodynamics, and Biological Functions of RNA Hairpins.

Bevilacqua PC, Blose JM

Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 pcb@chem.psu.edu.

blacksquare, square, filled Abstract Most RNA comprises one strand and therefore can fold back on itself to form complex structures. At the heart of these structures is the hairpin, which is composed of a stem having Watson-Crick base pairing and a loop wherein the backbone changes directionality. First, we review the structure of hairpins including diversity in the stem, loop, and closing base pair. The function of RNA hairpins in biology is discussed next, including roles for isolated hairpins, as well as hairpins in the context of complex tertiary structures. We describe the kinetics and thermodynamics of hairpin folding including models for hairpin folding, folding transition states, and the cooperativity of folding. Lastly, we discuss some ways in which hairpins can influence the folding and function of tertiary structures, both directly and indirectly. RNA hairpins provide a simple means of controlling gene expression that can be understood in the language of physical chemistry. Expected final online publication date for the Annual Review of Physical Chemistry Volume 59 is March 31, 2008. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

Published 16 October 2007 in Annu Rev Phys Chem.
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