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
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Research Support, Non-U.S. Gov't
MeSH terms
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Alkylating Agents / chemistry
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Alkylating Agents / metabolism
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Edetic Acid / chemistry
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Edetic Acid / metabolism
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Ferrous Compounds / chemistry
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Ferrous Compounds / metabolism
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Ligands*
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Molecular Probes* / chemistry
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Molecular Probes* / metabolism
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Peroxynitrous Acid / chemistry
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Peroxynitrous Acid / metabolism
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RNA, Ribosomal / metabolism*
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Reproducibility of Results
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Ribosomes / metabolism*
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Sulfuric Acid Esters / chemistry
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Sulfuric Acid Esters / metabolism
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Time Factors
Substances
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Alkylating Agents
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Ferrous Compounds
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Ligands
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Molecular Probes
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RNA, Ribosomal
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Sulfuric Acid Esters
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Peroxynitrous Acid
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Fe(II)-EDTA
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Edetic Acid
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dimethyl sulfate