Skip Navigation



Bioinformatics Advance Access published online on January 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl024
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/10/1177    most recent
btl024v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Mückstein, U.
Right arrow Articles by Hofacker, I. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Mückstein, U.
Right arrow Articles by Hofacker, I. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 18, 2005
Revised December 22, 2005
Accepted January 23, 2006

Article

Thermodynamics of RNA-RNA Binding

Ulrike Mückstein 1, Hakim Tafer 1, Jörg Hackermüller 2, Stephan H. Bernhart 1, Peter F. Stadler 3, and Ivo L. Hofacker 1 *

1 Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
2 Fraunhofer Institut für Zelltherapie und Immunologie - IZI, Deutscher Platz 5e, D-04103 Leipzig, Germany
3 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.; Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria; The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, New Mexico

* To whom correspondence should be addressed.
Ivo L. Hofacker, E-mail: ivo{at}tbi.univie.ac.at


  Abstract

Background: Reliable predictions of RNA-RNA binding energies is crucial e.g. for the understanding on RNAi, microRNA-mRNA binding, and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to "open" the binding site, and (2) the energy gained from hybridization.

Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired.

Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable to a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.

Availability: RNAup will be distributed as part of the Vienna RNA Package, www.tbi.univie.ac.at/ivo/RNA/.

Associate Editor: Thomas Lengauer
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
F. W. D. Huang, J. Qin, C. M. Reidys, and P. F. Stadler
Partition function and base pairing probabilities for RNA-RNA interaction prediction
Bioinformatics, October 15, 2009; 25(20): 2646 - 2654.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
C. Romero-Lopez and A. Berzal-Herranz
A long-range RNA-RNA interaction between the 5' and 3' ends of the HCV genome
RNA, September 1, 2009; 15(9): 1740 - 1752.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Chitsaz, R. Salari, S. C. Sahinalp, and R. Backofen
A partition function algorithm for interacting nucleic acid strands
Bioinformatics, June 15, 2009; 25(12): i365 - i373.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. G. Leparc, T. Tuchler, G. Striedner, K. Bayer, P. Sykacek, I. L. Hofacker, and D. P. Kreil
Model-based probe set optimization for high-performance microarrays
Nucleic Acids Res., February 1, 2009; 37(3): e18 - e18.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Pichon and B. Felden
Small RNA gene identification and mRNA target predictions in bacteria
Bioinformatics, December 15, 2008; 24(24): 2807 - 2813.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
W. Kong, H. Yang, L. He, J.-j. Zhao, D. Coppola, W. S. Dalton, and J. Q. Cheng
MicroRNA-155 Is Regulated by the Transforming Growth Factor {beta}/Smad Pathway and Contributes to Epithelial Cell Plasticity by Targeting RhoA
Mol. Cell. Biol., November 15, 2008; 28(22): 6773 - 6784.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Tafer and I. L. Hofacker
RNAplex: a fast tool for RNA-RNA interaction search
Bioinformatics, November 15, 2008; 24(22): 2657 - 2663.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. R. Gruber, R. Lorenz, S. H. Bernhart, R. Neubock, and I. L. Hofacker
The Vienna RNA Websuite
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W70 - W74.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y.-K. Park, S.-M. Park, Y.-C. Choi, D. Lee, M. Won, and Y. J. Kim
AsiDesigner: exon-based siRNA design server considering alternative splicing
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W97 - W103.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nikolajewa, R. Pudimat, M. Hiller, M. Platzer, and R. Backofen
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W688 - W693.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Ladunga
More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature
Nucleic Acids Res., January 28, 2007; 35(2): 433 - 440.
[Abstract] [Full Text] [PDF]


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.