title: Preferential activation of the 8-17 deoxyribozyme by Ca(2+) ions. Evidence for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme.
abstract: The 8-17 deoxyribozyme is a small RNA-cleaving DNA molecule of potential therapeutic interest. Here, the cleavage rates of 16 variants of the 8-17 deoxyribozyme were measured in the presence of different divalent metal ions. Despite the fact that 8-17 was originally selected in vitro for activity in the presence of Mg(2+) (Santoro, S. W., and Joyce, G. F. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 4262-4266) nearly all the 8-17 variants exhibited substantially higher (up to 20-fold) reaction rates in Ca(2+) as compared with Mg(2+). This preference for calcium ions critically depended on the nucleoside residues at two specific positions of the deoxyribozyme core. The Ca(2+) specificity of 8-17 is strongly reminiscent of the properties of Mg5, an RNA phosphodiester-cleaving deoxyribozyme previously isolated by Faulhammer and Famulok (Faulhammer, D., and Famulok, M. (1996) Angew. Chem. Int. Ed. Engl. 35, 2837-2841). Indeed, analysis of the Mg5 sequence revealed the presence of a complete 8-17 motif, coincident with the conserved region of Mg5. An 8-17 deoxyribozyme modeled after the Mg5 conserved region displayed catalytic features comparable with those reported for the full-length Mg5 deoxyribozyme.
authors.affiliation: Institute of Biochemical Sciences, University of Parma, 43100 Parma, Italy. peracchi@ipruniv.cce.unipr.it
authors.forename: A
authors.initials: A
authors.lastname: Peracchi
mesh_terms: D001483:Base Sequence; D002118:Calcium / Q000378:metabolism*; D020134:Catalytic Domain; D017124:Conserved Sequence; D021881:DNA, Catalytic; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004789:Enzyme Activation; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008345:Manganese / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation
chemical_list: D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; C407482:RNA-cleaving DNA 8-17; D008345:Manganese; D008274:Magnesium; D002118:Calcium