title: Biochemical analysis of hatchet self-cleaving ribozymes.
abstract: Hatchet RNAs are members of a novel self-cleaving ribozyme class that was recently discovered by using a bioinformatics search strategy. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides interspersed among bulges linking four base-paired substructures. A representative hatchet ribozyme from a metagenomic source requires divalent ions such as Mg(2+) to promote RNA strand scission with a maximum rate constant of ∼4 min(-1). As with all other small self-cleaving ribozymes discovered to date, hatchet ribozymes employ a general mechanism for catalysis involving the nucleophilic attack of a ribose 2'-oxygen atom on an adjacent phosphorus center. Kinetic characteristics of the reaction demonstrate that members of this ribozyme class have an essential requirement for divalent metal ions and that they might have a complex active site that employs multiple catalytic strategies to accelerate RNA cleavage by internal phosphoester transfer.
authors.affiliation: Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Sanshu
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Christina E
authors.initials: CE
authors.lastname: Lünse
authors.affiliation: Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Harris
authors.affiliation: Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D001483:Base Sequence; D002384:Catalysis; D020134:Catalytic Domain / Q000235:genetics; D002413:Cations, Divalent / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D016384:Consensus Sequence / Q000235:genetics; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000235:genetics; D012313:RNA / Q000235:genetics*; D016337:RNA, Catalytic / Q000235:genetics*; D013379:Substrate Specificity / Q000235:genetics
chemical_list: D002413:Cations, Divalent; D009711:Nucleotides; D016337:RNA, Catalytic; D012313:RNA
keywords: RNA cleavage; RNA processing; comparative sequence analysis; phosphoester transfer; phosphorothioate