Published online 18 May 2006
Article |
Predicting RNA pseudoknot folding thermodynamics
Department of Physics and Department of Biochemistry, University of Missouri-Columbia Columbia, MO 65211, USA
*To whom correspondence should be addressed. Tel: +1 573 882 6626; Fax: +1 573 882 4195; Email: chenshi{at}missouri.edu
Received March 24, 2006. Revised April 10, 2006. Accepted April 18, 2006.
Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease.
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