Recent genome and transcriptome sequencing projects have unveiled a plethora of highly structured RNA molecules as central mediators of cellular function. Single molecule Forster Resonance Energy Transfer (smFRET) is a powerful tool for analyzing the temporal evolution of the global structure of individual RNA molecules, in pursuit of understanding their essential structure-dynamics-function relationships. In contrast to enzymatic and chemical footprinting, NMR spectroscopy and X-ray crystallography, smFRET yields temporally resolved, quantitative information about single molecules rather than only time and ensemble averages of entire populations. This enables unique observations of transient and rare conformations under both equilibrium and non-equilibrium conditions.
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