title: Chemical probes for higher-order structure in RNA.
abstract: Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0 degrees C and 90 degrees C and at pH 4.5--8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNAPhe terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved.
mesh_terms: D000477:Alkylating Agents; D055598:Chemical Phenomena; D002621:Chemistry; D004047:Diethyl Pyrocarbonate; D006834:Hydrazines; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010649:Phenylalanine; D012313:RNA; D012331:RNA, Fungal; D012343:RNA, Transfer; D012441:Saccharomyces cerevisiae; D013463:Sulfuric Acid Esters
chemical_list: D000477:Alkylating Agents; D006834:Hydrazines; D012331:RNA, Fungal; D013463:Sulfuric Acid Esters; D010649:Phenylalanine; D012313:RNA; D012343:RNA, Transfer; C007482:dimethyl sulfate; D004047:Diethyl Pyrocarbonate