A New Approach to Model and Directly Control Co-Transcriptional RNA Folding

Abstract

RNAs are synthesized exclusively in a 5' to 3' direction and it is well established that many (particularly long noncoding, but also riboswitch) RNAs begin to fold before the transcript is fully synthesized. Indeed, in many cases, directional folding is thought to limit the formation of nonproductive, nonnative structures that might arise from a more random condensation of secondary and tertiary structures or to facilitate formation of necessary (and transient on pathway) folding intermediates. Site-specifically programmed pauses in transcription are often necessary to direct these interactions.Using tools from synthetic biology and nucleic acid nanotechnology, we are developing an alternative approach to direct and control 5' to 3' sequential RNA folding. The approach allows the introduction of pauses into the sequential release and allows the experimenter to halt and then resume RNA release/folding. Initial studies use the malachite green binding RNA aptamer, with a simple fluorescence readout of formation of the final structure. Subsequent studies will footprint intermediates with a variety of probes to follow the progress of folding and detect intermediates.View Large Image | View Hi-Res Image | Download PowerPoint Slide