title: A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity.
abstract: Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag+-specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag+. Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag+binding is unrelated to C-Ag+-C interaction. Its activity is enhanced by increasing Na+concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li+> Na+> K+. Ag10c binds one Na+ion and two Ag+ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na+interacts with the pro-Rpoxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag+ions. Therefore, Ag+exerts its function allosterically, while the scissile phosphate interacts with Na+, Li+, Na+, or Mg2+. This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag+aptamer.
authors.affiliation: Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada.
authors.forename: Runjhun
authors.initials: R
authors.lastname: Saran
authors.affiliation: Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Kleinke
authors.affiliation: Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada.
authors.forename: Wenhu
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada.
authors.forename: Tianmeng
authors.initials: T
authors.lastname: Yu
authors.affiliation: Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada.
authors.forename: Juewen
authors.identifier: 0000-0001-5918-9336
authors.initials: J
authors.lastname: Liu
mesh_terms: D000494:Allosteric Regulation; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism; D020029:Base Pairing; D001483:Base Sequence; D055162:Biocatalysis; D002413:Cations, Divalent; D002414:Cations, Monovalent; D018983:DNA Footprinting; D021881:DNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008094:Lithium / Q000737:chemistry / Q000378:metabolism; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry* / Q000378:metabolism; D011188:Potassium / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012834:Silver / Q000737:chemistry* / Q000378:metabolism; D012964:Sodium / Q000737:chemistry / Q000378:metabolism; D013463:Sulfuric Acid Esters / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D002413:Cations, Divalent; D002414:Cations, Monovalent; D021881:DNA, Catalytic; D010710:Phosphates; D013463:Sulfuric Acid Esters; D012834:Silver; D012313:RNA; D008094:Lithium; D012964:Sodium; D008274:Magnesium; C007482:dimethyl sulfate; D011188:Potassium