Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA

Ted Powers, Harry F. Noller

Research output: Contribution to journalArticlepeer-review

198 Scopus citations


Complexes between 168 rRNA and purified ribosomal proteins, either singly or in combination, were assembled in vitro and probed with hydroxyl radicals generated from free Fe(II)-EDTA. The broad specificity of hydroxyl radicals for attack at the ribose moiety in both single- and double-stranded contexts permitted probing of nearly all of the nucleotides in the 16S rRNA chain. Specific protection of localized regions of the RNA was observed in response to assembly of most of the ribosomal proteins. The locations of the protected regions were in good general agreement with the footprints previously reported for base-specific chemical probes, and with sites of RNA-protein crosslinking. New information was obtained about interaction of ribosomal proteins with 16S rRNA, especially with helical elements of the RNA. In some cases, 5′ or 3′ stagger in the protection pattern on complementary strands suggests interaction of proteins with the major or minor groove, respectively, of the RNA. These results reinforce and extend previous data on the localization of ribosomal proteins with respect to structural features of 16S rRNA, and offer many new constraints for three-dimensional modeling of the 30S ribosomal subunit.

Original languageEnglish (US)
Pages (from-to)194-209
Number of pages16
Issue number2
StatePublished - 1995


  • Fe-EDTA
  • Primer extension
  • Protein-RNA interactions
  • Ribonucleoprotein
  • Ribosome assembly

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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