Methods for Comprehensive RNA Structure and Dynamics Analysis using SHAPE Technologies

Steen-Burrell, Kady-Ann Camele

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March 22, 2019

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Steen-Burrell, Kady-Ann Camele
- Affiliation: College of Arts and Sciences, Department of Chemistry

Abstract

The many important cellular functions of RNA molecules depend on formation of complex RNA secondary and tertiary structures. The formation of these structures is facilitated by the intrinsic motion of RNA nucleotides and can be influenced by various ligand or protein interactions. RNA SHAPE technology has made the determination of many RNA secondary structures facile. However, the applicability of traditional SHAPE technology to short RNAs (less than 100 nucleotides) in their native state is limited by primer extension detection. Additionally, it is often difficult to discern the structural context of constrained nucleotides in a traditional SHAPE experiment. In this work, I first develop an alternate SHAPE 2'-O-adduct detection method, termed RNase-detected SHAPE, which takes advantage of the RNA-specific activity of an exoribonuclease, RNase R. In the presence of a SHAPE 2'-O-adduct or adducts at the nucleotide base-pairing face, RNase R stops three or four nucleotides 3' of the modification site, respectively. RNase-detected SHAPE allowed for the structural characterization of a small, biologically relevant riboswitch in its ligand-free state and identification of a bulge register shift that facilitates formation of the ligand-bound state. Second, I develop a method for the de novo identification of nucleotides involved in, or adjacent to, key RNA tertiary structure interactions, termed differential SHAPE reactivity analysis. This method uses two SHAPE electrophiles, N-methylisatoic anhydride (NMIA) and 1-methyl-6-nitroisatoic anhydride (1M6) that detect slowly dynamic and one-sided stacking nucleotides, respectively. Together, both types of nucleotide behaviors provide a RNA tertiary structure "fingerprint" since both tend to be over-represented in tertiary structure interactions and motifs. Third, I develop a chemical method for the removal of SHAPE 2'-O-adducts by ester bond cleavage while limiting RNA phosphodiester backbone degradation which allows for the downstream manipulation of previously modified RNA. The extent of SHAPE 2'-O-adduct removal can be modulated by varying the concentration of hydroxylamine and reaction times. Finally, I evaluate the ability of SHAPE chemistry to detect ligand-induced conformational changes by comparing SHAPE reactivities and NMR measurements. Dynamics as measured by SHAPE reactivities and the NMR order parameter, S2, correlate well for small molecule binding to RNA.

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