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Bioinformatics Advance Access published online on November 4, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp627
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

Robert A. Forties 1 and Ralf Bundschuh 1,2,3,*

1Department of Physics, The Ohio State University
2Center for RNA Biology, The Ohio State University
3Department of Biochemistry, The Ohio State University

*To whom correspondence should be addressed. Ralf Bundschuh, E-mail: bundschuh{at}mps.ohio-state.edu


  Abstract

Motivation: There are many important proteins which bind singlestranded nucleic acids, such as the nucleocapsid protein in HIV and the RecA DNA repair protein in bacteria. The presence of such proteins can strongly alter the secondary structure of the nucleic acid molecules. Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to fully understanding many biological processes.

Results: We develop a model for predicting nucleic acid secondary structure in the presence of single stranded binding proteins, and implement it as an extension of the Vienna RNA Package. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously determined. This leaves the footprint and sequence dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid, and FRET distributions for fluorophores attached to the nucleic acid.

Availability: Source code for our modified version of the Vienna RNA package is freely available at http://bioserv.mps.ohio-state.edu/Vienna+P, implemented in C and running on Linux.

Contact: bundschuh{at}mps.ohio-state.edu

Associate Editor: Prof. Ivo Hofacker

Received on September 10, 2009; revised on October 28, 2009; accepted on November 1, 2009

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