Prediction of co-transcriptional RNA Folding for Modeling Riboswitches
RNA molecules start forming secondary structure as soon as they emerge from the polymerase complex during transcription. This co-transcriptional folding can lead to RNAs that are kinetically trapped in non-equilibrium states. Such kinetic folding aspects cannot be captured by the commonly used dynamic programming algorithms for RNA secondary structure prediction, but require computationally more expensive methods for simulating folding kinetics. The talk will present novel and fast co-transcriptional folding heuristic that can be used on sequences of several hundred nucleotides and thus cover the typical size of riboswitches. We will show how these methods can be used to successfully model the behavior of transcriptional riboswitches, whose function depends on the precise timing of the formation of terminator hairpins in the presence or absence of the riboswitch ligand.