Georgia Institute of Technology College of Sciences

The prediction of RNA secondary structures from sequence is a well developed task in computational RNA Biology. However, in a cellular environment RNA molecules are not isolated but rather interact with a multitude of proteins. RNA secondary structure affects those interactions with proteins and vice versa proteins binding the RNA affect its secondary structure.  We have extended the dynamic programming approaches traditionally used to quantify the ensemble of RNA secondary structures in solution to incorporate protein-RNA interactions and thus quantify these effects of protein-RNA interactions and RNA secondary structure on each other. Using this approach we demonstrate that taking into account RNA secondary structure improves predictions of protein affinities from RNA sequence, that RNA secondary structures mediate cooperativity between different proteins binding the same RNA molecule, and that sequence variations (such as Single Nucleotide Polymorphisms) can affect protein affinity at a distance mediated by RNA secondary structures.

https://gatech.bluejeans.com/348270750