title: In vivo detection of ribozyme cleavage products and RNA structure by use of terminal transferase-dependent PCR.
abstract: Terminal transferase-dependent PCR (TDPCR) can be used after reverse transcription to analyze RNA. This method (RT-TDPCR) is able to provide in vivo information at nucleotide-level resolution, and has been used for study of ribozymes, RNA size, RNA structure, and RNA-protein interactions. A detailed protocol of RT-TDPCR is presented here with examples of its use in detecting ribozyme cleavage intermediates in yeast and a RNA transcription start site in mammalian cells.
authors.affiliation: Department of Biology and Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
authors.forename: Hsiu-Hua
authors.initials: HH
authors.lastname: Chen
authors.forename: Daniela
authors.initials: D
authors.lastname: Castanotto
authors.forename: Jeanne
authors.initials: J
authors.lastname: LeBon
authors.forename: John J
authors.initials: JJ
authors.lastname: Rossi
authors.forename: Arthur D
authors.initials: AD
authors.lastname: Riggs
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D007202:Indicators and Reagents; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction / Q000379:methods; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D017931:DNA Primers; D007202:Indicators and Reagents; D016337:RNA, Catalytic; D012313:RNA