Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer.
Tertiary contacts are critical to stabilizing the folded conformations of structured RNAs. In some cases, these contacts have been shown to interact with positive cooperativity. Measuring the energetic coupling of tertiary contact formation is among the most basic physical characterizations of a structured RNA. With proper experimental design, single-molecule fluorescence resonance energy transfer (smFRET) allows the rigorous determination of the energetic coupling. This chapter aims to provide a general experimental approach to measuring the energetic coupling of tertiary contacts, using smFRET.
Greenfeld
Max
M
Department of Chemical Engineering, Stanford University, Stanford, California, USA.
Herschlag
Daniel
D
D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
D012313:RNA