RNA Secondary Structure Prediction in the Presence of Single-Stranded Binding Proteins

Secondary structure prediction of RNA molecules is a problem in Bioinformatics with several well established solutions. However, while the approaches to RNA secondary structure prediction are successful in describing RNA molecules in vitro, RNA molecules in vivo often assume their secondary structure while interacting with many other consitutents of the cell. One of those constitutents that have the ability to significantly alter RNA secondary structure formation are proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV or the RecA DNA repair protein in bacteria. We extend established secondary structure prediction methods to explicitly include the effect of such interactions. Using our model we are able to predict the probability of proteins binding at any position in the nucleic acid sequence as well as the impact of the protein on nucleic acid base pairing and on the end-to-end distance distribution of the nucleic acid.