Complementing global measures of RNA folding with local reports of backbone solvent accessibility by time resolved hydroxyl radical footprinting

Jörg C. Schlatterer, Michael D. Brenowitz

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

A variety of analytical techniques are used to probe the mechanisms by which RNA molecules fold to discrete three dimensional structures. Methods such as small angle X-ray scattering (SAXS) report global properties like overall size and shape of the RNA. Other methods such as chemical or enzymatic mapping (footprinting) report properties with resolution as fine as single nucleotide. The hydroxyl radical (•OH) is a footprinting probe which cleaves the oligonucleotide backbone independently of sequence and thus is a valuable reporter of backbone solvent accessibility. Combinations of global and local measures of folding reactions are uniquely able to distinguish specific from nonspecific processes. This article highlights the application of •OH footprinting as a complement to SAXS for kinetics analysis of RNA folding. We illustrate this combination of techniques using a study of the role played by the stiffness of a hinge in determining the rate limiting step of a Mg2+-mediated RNA folding reaction.

Original languageEnglish (US)
Pages (from-to)142-147
Number of pages6
JournalMethods
Volume49
Issue number2
DOIs
StatePublished - Oct 2009

Fingerprint

RNA Folding
Hydroxyl Radical
X-Rays
RNA
X ray scattering
Oligonucleotides
Nucleotides
Hinges
Stiffness
Molecules
Kinetics

Keywords

  • Footprinting
  • Hydroxyl radical
  • RNA folding
  • SAXS

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Complementing global measures of RNA folding with local reports of backbone solvent accessibility by time resolved hydroxyl radical footprinting. / Schlatterer, Jörg C.; Brenowitz, Michael D.

In: Methods, Vol. 49, No. 2, 10.2009, p. 142-147.

Research output: Contribution to journalArticle

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