title: Identification of the Same Na(+)-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions.
abstract: We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na(+) and reported to be highly selective for Na(+) over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce(4+) and found to be active with trivalent lanthanides, Y(3+) and Pb(2+). Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60% sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na(+) is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na(+). Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na(+) and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na(+)-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Seyed-Fakhreddin
authors.initials: SF
authors.lastname: Torabi
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. yi-lu@illinois.edu.|Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. yi-lu@illinois.edu.
authors.forename: Yi
authors.initials: Y
authors.lastname: Lu
mesh_terms: D002414:Cations, Monovalent / Q000378:metabolism; D021881:DNA, Catalytic / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012260:Ribonucleases / Q000378:metabolism*; D052156:SELEX Aptamer Technique; D012964:Sodium / Q000378:metabolism*
chemical_list: D002414:Cations, Monovalent; D021881:DNA, Catalytic; D012964:Sodium; D012260:Ribonucleases
keywords: DNAzyme (deoxyribozyme); Functional motif; In vitro selection; Lanthanides; Sodium