Structural analysis of RNA in living cells by in vivo synchrotron X-ray footprinting.

Tadepalli Adilakshmi, Sarah F.C. Soper, Sarah A. Woodson

Research output: Contribution to journalArticle

Abstract

Chemical footprinting methods are widely used to probe the solution structures of nucleic acids and their complexes. Among the many available modifying reagents, hydroxyl radical is exceptional in its ability to provide nucleotide-level information on the solvent accessibility of the nucleic acid backbone. Until recently, hydroxyl radical footprinting has been limited to in vitro experiments. We describe the use of synchrotron X-radiation to generate hydroxyl radicals within cells for effective footprinting of RNA-protein complexes in vivo. This technique gives results that are consistent with in vitro footprinting experiments, with differences reflecting apparent structural changes to the RNA in vivo.

Original languageEnglish (US)
Pages (from-to)239-258
Number of pages20
JournalMethods in enzymology
Volume468
StatePublished - 2009

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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    Adilakshmi, T., Soper, S. F. C., & Woodson, S. A. (2009). Structural analysis of RNA in living cells by in vivo synchrotron X-ray footprinting. Methods in enzymology, 468, 239-258.