Characterization of a DNA-cleaving deoxyribozyme.
A copper-dependent self-cleaving DNA that was isolated by in vitro selection has been minimized to its smallest active domain using both in vitro selection and rational design methods. The minimized 46-nucleotide deoxyribozyme forms duplex and triplex substructures that flank a highly conserved catalytic core. This self-cleaving construct can be converted into a bimolecular complex that comprises separate substrate and enzyme domains. Substrate cleavage is directed at one of two adjacent nucleotides and proceeds via an oxidative cleavage mechanism that is unique to the position cleaved. The structural, kinetic and mechanistic characteristics of this DNA-cleaving deoxyribozyme are reported.
Carmi
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Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.
Breaker
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D001483:Base Sequence; D002384:Catalysis; D003300:Copper / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D021881:DNA, Catalytic / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D003839:Deoxyadenosines / Q000737:chemistry; D003854:Deoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010084:Oxidation-Reduction; D017422:Sequence Analysis, DNA; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D003839:Deoxyadenosines; D003854:Deoxyribonucleotides; D003300:Copper; D004247:DNA; C058118:2'-deoxyadenosine