Abstract
RNA molecules perform a wide variety of functions to control many cellular pathways. Critical to these roles is the ability of an RNA to fold into complex three-dimensional structures. As part of this folding, unique elements of RNA structure become more exposed or hidden to solvent and these properties are important to understand an RNAs final fold. Characterizing solvent accessibility can enable researchers to better understand the overall fold of an RNA and how it interacts with trans acting factors, such as proteins. Herein we describe the methods toward using light activated structural evaluation of RNA, or LASER, which measures purine nucleobase solvent accessibility. To date, LASER has been used inside and outside of cells to measure RNA solvent accessibility and RNA interactions with proteins.
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