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.
RNA–RNA interactions RNA ligation RNA labeling Single molecule FRET
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This work was supported by an NSF CAREER award (MCB-115343). P.C. is a Pew Scholar in the Biomedical Sciences.
Kinoshita Y, Nishigaki K, Husimi Y (1997) Fluorescence-, isotope- or biotin-labeling of the 5'-end of single-stranded DNA/RNA using T4 RNA ligase. Nucleic Acids Res 25(18):3747–3748PubMedCentralPubMedCrossRefGoogle Scholar
Solomatin S, Herschlag D (2009) Methods of site-specific labeling of RNA with fluorescent dyes. Methods Enzymol 469:47–68PubMedCrossRefGoogle Scholar
Joo C, Ha T (2012) Labeling DNA (or RNA) for single-molecule FRET. Cold Spring Harb Protoc 2012(9):1005–1008PubMedGoogle Scholar
Joo C, Ha T (2012) Preparing sample chambers for single-molecule FRET. Cold Spring Harb Protoc 2012(10):1104–1108PubMedGoogle Scholar
Diao J et al (2012) A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins. Nat Protoc 7(5):921–934PubMedCrossRefGoogle Scholar