Single ribozyme molecules

Zhuang, XW, Kim, H, Pereira, MJB, Babcock, HP, Walter, NG,and Chu, S, Correlating structural dynamics and function in single ribozyme molecules. Science 296 (2002) 1473-1476. 

Figure 6.17 Docked states have a strong memory effect, as indicated by FRET time traces of single rlbozyme-substrate complexes, (a) Memory effect of the undocking kinetics where a molecule rarely switches between different docked states. (b)An example of memory loss after 3 h. The excitation was shut off after 500 s for 3 h to prevent dye photobleaching. Reprinted with permission from Zhuang etal., Correlating structural dynamics and function in single ribozyme molecules. Science 296 (2003) 1473-1476. Copyright 2002 AAAS.

The importance of water molecules for the structural dynamics and the functioning of ribozymes was investigated by Rhodes and co-workers. They studied non-coded RNA using a combination of explicit solvent molecular dynamics and single molecule fluorescence spectroscopy approaches (Rhodes et al 2006). 

Xie, Z., Srividya, N., Sosnick, T. R., Pan, T., and Scherer, N. F. (2004). Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc. Natl. Acad. Sci. USA 101, 534-539. 

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.,... 

Okumus, B., Wilson, T. J., Lilley, D. M. J., and Ha, T. (2004). Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. Biophys. J. 87,... 

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