Skip Navigation


Nucleic Acids Research Advance Access originally published online on June 9, 2009
Nucleic Acids Research 2009 37(14):4696-4706; doi:10.1093/nar/gkp465
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (785K) Freely available
Right arrow Screen PDF (800K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/14/4696    most recent
gkp465v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Christiansen, M. E.
Right arrow Articles by Znosko, B. M.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Christiansen, M. E.
Right arrow Articles by Znosko, B. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2009, Vol. 37, No. 14 4696-4706
© 2009 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

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

Martha E. Christiansen and Brent M. Znosko*

Department of Chemistry, Saint Louis University, St Louis, MO 63103, USA

*To whom correspondence should be addressed. Tel: +1 314 977 8567; Fax: +1 314 977 2521; Email: znoskob{at}slu.edu

Received March 6, 2009. Revised May 4, 2009. Accepted May 15, 2009.

Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329–4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.