Single molecule studies of RNA-RNA interactions

Abstract

Non-coding RNAs including microRNAs, siRNAs, and snoRNAs interact with their targets directly through RNA-RNA interactions by base-paring (van Himbergen et al., Nucleic Acids Res 21(8):1713-1717, 1993). RNA-RNA interactions play important roles in gene transcription and protein translation, which can be investigated with several experimental techniques including single molecule methods. Here, we describe how single molecule Förster resonance energy transfer (FRET) can be used to study RNA-RNA interactions in vitro by either surface immobilization or vesicle encapsulation.