title: Hammerhead ribozymes with a faster cleavage rate.
abstract: A hammerhead ribozyme that was previously reported to have a rate of chemical cleavage 10-fold faster than that of conventional hammerheads was analyzed in greater detail. Although originally found as a bimolecular hammerhead assembled through helices I and II, fast cleavage was observed in hammerheads in the more conventional helix I-helix III form, provided the sequence of helix I of teh fast hammerhead was preserved. Mutations indicted that the fast rate of cleavage was due to the presence of both the U1.1-A2.1 and A1.2-U2.2 base pairs. The faster rate of cleavage was due to a small increase in the activation entropy of the reaction. In addition, we confirmed previous reports that increasing the length of helix I by greater than five base pairs inhibits cleavage slightly and have uncovered a similar effect in helix II.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA.
authors.forename: B
authors.initials: B
authors.lastname: Clouet-d'Orval
authors.forename: O C
authors.initials: OC
authors.lastname: Uhlenbeck
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002384:Catalysis; D007700:Kinetics; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D016337:RNA, Catalytic