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Nucleic Acids Research Advance Access originally published online on September 18, 2006
Nucleic Acids Research 2006 34(17):4912-4924; doi:10.1093/nar/gkl472
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Nucleic Acids Research, 2006, Vol. 34, No. 17 4912-4924
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

Zhi John Lu, Douglas H. Turner1 and David H. Mathews*

Department of Biochemistry & Biophysics and Center for Pediatric Biomedical Research, University of Rochester Medical Center 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA 1 Department of Chemistry, University of Rochester Box 0216, Rochester, NY 14627, USA

*To whom correspondence should be addressed. Tel: 1 585 275 1734; Fax: 1 585 275 6007; Email: david_mathews{at}urmc.rochester.edu

Received March 27, 2006. Revised June 20, 2006. Accepted June 20, 2006.

A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures.


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