Real-time dynamics of ribosome-ligand interaction by time-resolved chemical probing methods

Methods Enzymol. 2007:430:45-58. doi: 10.1016/S0076-6879(07)30003-7.

Abstract

Three protocols to perform time-resolved in situ probing of rRNA are described. The three methods (chemical modification with DMS and rRNA backbone cleavage by hydroxyl radicals generated by either K-peroxonitrite or Fe(II)-EDTA) make use of a quench-flow apparatus and exploit reactions that are faster than the interactions of ribosomal subunits with their ligands. These methods allow the investigation of the path and dynamics, in a approximately equal 50 to 1500ms time range, of the binding and dissociation of ribosomal ligands.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alkylating Agents / chemistry
  • Alkylating Agents / metabolism
  • Edetic Acid / chemistry
  • Edetic Acid / metabolism
  • Ferrous Compounds / chemistry
  • Ferrous Compounds / metabolism
  • Ligands*
  • Molecular Probes* / chemistry
  • Molecular Probes* / metabolism
  • Peroxynitrous Acid / chemistry
  • Peroxynitrous Acid / metabolism
  • RNA, Ribosomal / metabolism*
  • Reproducibility of Results
  • Ribosomes / metabolism*
  • Sulfuric Acid Esters / chemistry
  • Sulfuric Acid Esters / metabolism
  • Time Factors

Substances

  • Alkylating Agents
  • Ferrous Compounds
  • Ligands
  • Molecular Probes
  • RNA, Ribosomal
  • Sulfuric Acid Esters
  • Peroxynitrous Acid
  • Fe(II)-EDTA
  • Edetic Acid
  • dimethyl sulfate