2-aminopurine fluorescence as a probe of local RNA structure and dynamics and global folding

Michael J. Rau, Kathleen B. Hall

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

3 Scopus citations


The biology of an RNA is encoded in its structure and dynamics, whether that be binding to a protein, binding to another RNA, enzymatic catalysis, or becoming a substrate. In solution, most RNA molecules are sampling conformations, and their structures are best described as conformational ensembles. For larger RNAs, experiments that can describe the conformations of their domains can be particularly daunting, especially when the RNA is novel and not well characterized. Here, we explain how we have used site-specific 2-aminopurine as a fluorescent probe of the secondary and tertiary structures of a 60 nucleotide RNA, and what new findings we have about its Mg2+ -dependent conformational changes. We focus on this RNA from prokaryotic ribosome as a proof of concept as well as a research project. Its tertiary structure is known from a cocrystal, and its secondary structure is modeled from phylogenetic conservation, but there are virtually no data describing the motions of its nucleotides in solution, or its folding kinetics. It is a perfect system to illustrate the unique information that comes from a comprehensive fluorescence study of this intricate RNA.

Original languageEnglish
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Number of pages26
StatePublished - 2015

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988


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