Single-molecule FRET

Nir, E., Michalet, X., Hamadani, K. M., Laurence, T. A., Neuhauser, D., Kovchegov, Y. and Weiss, S. (2006). Shot-noise limited single-molecule FRET histograms Comparison between theory and experiments. J. Phys. Chem. B 110, 22103-24. 

Conformational Structure and Dynamics from Single-Molecule FRET... 

The plan of the remainder of this paper is as follows. Different ways of measuring conformational structure and dynamics via single-molecule FRET are described in Sec. 2 and demonstrated on the two-stranded coiled-coil polypeptide model in Sec. 3. The results are summarized and discussed in Sec. 4. 

Measurement of conformational structure and dynamics via single-molecule FRET... 

We have developed the splinted RNA ligation procedure outlined in this chapter to generate site-specifically dye-labeled telomerase RNA constructs. These modified telomerase RNA constructs may be used to characterize dynamic RNA structural properties using Forster resonance energy transfer (FRET) (Stone et al., 2007). Our laboratory specializes in single molecule FRET measurements, which facilitates the direct observation of transient RNA structural states. The details of single molecule FRET... 

Figure 2.6 Application of splinted RNA ligation procedure single molecule FRET. (A) Diagram of prism-type total internal reflection fluorescence microscope (TIRFM) for single molecule FRET measurements. (B) Distribution of single-molecule FRET values for dye-labeled telomerase RNA molecules generated by splinted RNA ligation. (C) Dye intensity and FRET traces of a single telomerase RNA molecule Cy3 emission (green), Cy5 emission (red), FRET ratio (blue).

Hengesbach, M., et al. (2008). RNA intramolecular dynamics by single-molecule FRET. Curr. Protoc. Nucleic Acid Chem. Chapter 11, Unit 11 12. 

A step by step overview of the process of obtaining RNA constructs ready for single molecule FRET is presented here. For each step, several alternative methods described in the literature are suggested. Means of... 

Hodak, J. H., Fiore, J. L., Nesbitt, D. J., Downey, C. D., and Pardi, A. (2005). Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Proc. Natl. Acad. Sci. USA 102, 10505-10510. 

Single-molecule FRET has been applied to the folding of the group I intron ribozyme (Lee et al, 2007a Russell et al, 2002 Zhuang et al, 2000), the group II intron ribozyme (Steiner et al., 2008), the VS ribozyme (Pereira et al, 2008), and the interaction of a tetraloop and its receptor (Hodak et al.,... 

McKinney, S. A., Joo, C., and Ha, T. (2006). Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91, 1941—1951. 

Nienhaus GU. Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macro-mol. Biosci. 2006 6 907-922. 

Single-molecule FRET has been used to study the kinetics of unfolding of the human telomeric intramolecular G-quadruplex, the DNA-binding orientation of an E.coli REP monomer to a ss/ds DNA junction, four-way... 

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