title: A novel strategy of chemical modification for rate enhancement of 10-23 DNAzyme: a combination of A9 position and 8-aza-7-deaza-2'-deoxyadenosine analogs.
abstract: With the help of a divalent-metal ion, 10-23 DNAzyme cleaves RNA. Chemical modification of its catalytic loop to make a more efficient enzyme has been a challenge. Our strategy started from its five 2'-deoxyadenosine residues (A5, A9, A11, A12, and A15) in the loop based on the capability of the N7 atom to form hydrogen bonds in tertiary structures. 8-Aza-7-deaza-2'-deoxyadenosine and its analogs with 7-substituents (3-aminopropyl, 3-hydroxylpropyl, or phenethyl) were each used to replace five dA residues, respectively, and their effect on cleavage rate were evaluated under single-turnover conditions. The results indicated that the N7 atom of five dA residues were necessary for catalytic activity, and the N8 atom and 7-substituents were detrimental to the catalytic behavior of 10-23 DNAzyme, except that all these modifications at A9 were favourable for the activity. Especially, DZ-3-9 with 7-(3-aminopropyl)-8-aza-7-deaza-2'-deoxyadenosine (3) at A9 position gave a 12- fold increase of k(obs), compared to the corresponding parent 10-23 DNAzyme. DZ-3-9 was supposed to catalyze the cleavage reaction with the same mechanism as 10-23 DNAzyme based on their very similar pH-dependent and divalent metal ions-dependent cleavage patterns. Introduction of functional groups at A9 position was demonstrated to be a successful and feasible approach for more efficient 10-23 DNAzyme analogs.
authors.affiliation: Beijing Institute of Pharmacology and Toxicology, Beijing, China.
authors.forename: Junlin
authors.initials: J
authors.lastname: He
authors.forename: Di
authors.initials: D
authors.lastname: Zhang
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.forename: Xia
authors.initials: X
authors.lastname: Wei
authors.forename: Maosheng
authors.initials: M
authors.lastname: Cheng
authors.forename: Keliang
authors.initials: K
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D002413:Cations, Divalent / Q000378:metabolism; D021881:DNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism*; D003839:Deoxyadenosines / Q000737:chemistry* / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000378:metabolism
chemical_list: D002413:Cations, Divalent; D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D003839:Deoxyadenosines; C402582:RNA-cleaving DNA 10-23; D012313:RNA; C058118:2'-deoxyadenosine