Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease

Kady Ann Steen, Arun Malhotra, Kevin M. Weeks

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a powerful approach for characterizing RNA structure and dynamics at single-nucleotide resolution. However, SHAPE technology is limited, sometimes severely, because primer extension detection obscures structural information for ∼15 nts at the 5' end and 40-60 nts at the 3' end of the RNA. Moreover, detection by primer extension is more complex than the actual structure-selective chemical interrogation step. Here we quantify covalent adducts in RNA directly by adduct-inhibited exoribonuclease degradation. RNA 2'-O-adducts block proces-sivity of a 3'→5' exoribonuclease, RNase R, to produce fragments that terminate three nucleotides 3' of the modification site. We analyzed the structure of the native thiamine pyrophosphate (TPP) riboswitch aptamer domain and identified large changes in local nucleotide dynamics and global RNA structure upon ligand binding. In addition to numerous changes that can be attributed to ligand recognition, we identify a single nucleotide bulge register shift, distant from the binding site, that stabilizes the ligand-bound structure. Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) should prove broadly useful for facile structural analysis of small noncoding RNAs and for RNAs that have functionally critical structures at their 5' and 3' ends.

Original languageEnglish
Pages (from-to)9940-9943
Number of pages4
JournalJournal of the American Chemical Society
Volume132
Issue number29
DOIs
StatePublished - Jul 28 2010

Fingerprint

Exoribonucleases
Acylation
RNA
Hydroxyl Radical
Nucleotides
Ligands
Riboswitch
Thiamine Pyrophosphate
Small Untranslated RNA
Shift registers
Ribonucleases
Structural analysis
Binding sites
Binding Sites
Technology
Degradation

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease. / Steen, Kady Ann; Malhotra, Arun; Weeks, Kevin M.

In: Journal of the American Chemical Society, Vol. 132, No. 29, 28.07.2010, p. 9940-9943.

Research output: Contribution to journalArticle

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