Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation

Tadepalli Adilakshmi, Richard A. Lease, Sarah A. Woodson

Research output: Contribution to journalArticlepeer-review

Abstract

We used a high flux synchrotron X-ray beam to map the structure of 16S rRNA and RNase P in viable bacteria in situ. A 300 ms exposure to the X-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. The in vivo footprints of the 16S rRNA in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the RNA backbone to hydroxyl radical. Protection or enhanced cleavage of certain nucleotides in vivo can be explained by interactions with tRNA and perturbation of the subunit interface. Thus, short exposures to a synchrotron X-ray beam can footprint the tertiary structure and protein contacts of RNA-protein complexes with nucleotide resolution in living cells.

Original languageEnglish (US)
Article numbere64
JournalNucleic acids research
Volume34
Issue number8
DOIs
StatePublished - 2006

ASJC Scopus subject areas

  • Genetics

Fingerprint

Dive into the research topics of 'Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation'. Together they form a unique fingerprint.

Cite this