SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing

Timothy Wiryaman; Navtej Toor

doi:10.1007/978-1-0716-0716-9_10

SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing

Methods Mol Biol. 2021:2167:171-182. doi: 10.1007/978-1-0716-0716-9_10.

Authors

Timothy Wiryaman¹, Navtej Toor²

Affiliations

¹ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
² Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. ntoor@ucsd.edu.

Abstract

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a widely used technique for studying the structure and function of RNA molecules. It characterizes the flexibility of single nucleotides in the context of the local RNA structure. Here we describe the application of SHAPE-MaP (mutational profiling) to study different conformational states of the group II intron during the self-splicing reaction.

Keywords: Chemical structure probing; Group II intron; Next-generation sequencing; RNA structure; SHAPE-MaP.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Acylation
DNA Mutational Analysis / methods*
High-Throughput Nucleotide Sequencing / methods*
Introns / genetics*
Mutation
Nucleic Acid Conformation*
RNA / chemistry*
RNA / genetics
RNA Splicing / genetics*
Reverse Transcription
Sequence Analysis, RNA / methods*
Software

Substances

RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding