Structured RNA molecules play roles in central biological processes and understanding the basic forces and features that govern RNA folding kinetics and thermodynamics can help elucidate principles that underlie biological function. Here we investigate one such feature, the specific interaction of monovalent cations with a structured RNA, the P4–P6 domain of the Tetrahymena ribozyme. We employ single molecule FRET (smFRET) approaches as these allow determination of folding equilibrium and rate constants over a wide range of stabilities and thus allow direct comparisons without the need for extrapolation. These experiments provide additional evidence for specific binding of monovalent cations, Na+ and K+, to the RNA tetraloop–tetraloop receptor (TL–TLR) tertiary motif. These ions facilitate both folding and unfolding, consistent with an ability to help order the TLR for binding and further stabilize the tertiary contact subsequent to attainment of the folding transition state.
- ion atmosphere
- ribonucleic acid (RNA) folding
- single-molecule fluorescence resonance energy transfer (FRET)
- tertiary contact motif
Single Biomolecules – in silico, in vitro and in vivo: Held at the University of Hertfordshire, U.K., 11 - 13 September 2014.
Abbreviations: MC, metal core; MCR, metal core receptor; smFRET, single molecule FRET; TL, tetraloop; TLR, tetraloop receptor
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