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Methods. 2009 Oct;49(2):128-35. doi: 10.1016/j.ymeth.2009.04.001. Epub 2009 Apr 9.

Probing RNA conformational dynamics and heterogeneity using femtosecond time-resolved fluorescence spectroscopy.

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Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX 75083-0688, USA.


RNA structures are very dynamic and the dynamic motions result in a heterogeneous conformational ensemble. It is crucial to illustrate the role of conformational dynamics in RNA function. A variety of spectroscopic methods have been used to investigate the dynamic aspects of RNA structures. Recently, ultrafast time-resolved spectroscopy, a well-established technique, has been introduced as a new tool in this field. With femtosecond time-resolution, one can resolve the heterogeneous nature of RNA conformational ensemble quantitatively, detect and characterize minor unusual conformations, and capture folding events that may occur on a fast timescale. Here, we review the technical aspects of using an ultrafast fluorescence up-conversion technique to probe the heterogeneous base stacking patterns in RNA motifs and dynamic base motions that allow sampling of multiple states.

[Indexed for MEDLINE]

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