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. Author manuscript; available in PMC: 2016 Mar 4.
Published in final edited form as: Methods Enzymol. 2015 Feb 7;553:215–234. doi: 10.1016/bs.mie.2014.10.061

Figure 1.

Figure 1

Detecting nucleotide mobility experimentally and computationally. (a) Schematic for the acylation reaction and the 2'-hydroxyl group of an RNA nucleotide with the SHAPE reagent (NMIA). The acylation reaction is more probable when backbone is mobile and base is unpaired (b) Mobility of the 2'-hydroxyl group is characterized in molecular dynamics simulations using the RMS fluctuations of the angle between the 2'-hydroxyl group, phosphate group, and the 5' oxygen.