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

Methods in enzymology

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

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      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.

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      Journal
      10.1016/S0076-6879(07)30003-7
      17913634

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