Structural bioinformatics Pseudoknots in RNA folding landscapes

Motivation: The function of an RNA molecule is not only linked to its native structure, which is usu-ally taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the fold-ing process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these ques-tions. Efficient coarse-graining methods are required to reduce the intractably vast energy land-scapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuris-tic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary struc-tures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and system-atically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseu