Probing RNA conformational dynamics and heterogeneity using femtosecond time-resolved fluorescence spectroscopy.
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.
Zhao
Liang
L
Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX 75083-0688, USA.
Xia
Tianbing
T
D015075:2-Aminopurine / Q000737:chemistry; D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry; D016880:Anisotropy; D004867:Equipment Design; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*; D013050:Spectrometry, Fluorescence / Q000379:methods*; D013997:Time Factors
D012367:RNA, Viral; C043837:7-deazaadenine; D015075:2-Aminopurine; D006147:Guanine; D012313:RNA; C066856:7-deazaguanine; D000225:Adenine