title: Capping DNA with DNA.
abstract: Twelve classes of deoxyribozymes that promote an ATP-dependent "self-capping" reaction were isolated by in vitro selection from a random-sequence pool of DNA. Each deoxyribozyme catalyzes the transfer of the AMP moiety of ATP to its 5'-terminal phosphate group, thereby forming a 5',5'-pyrophosphate linkage. An identical DNA adenylate structure is generated by the T4 DNA ligase during enzymatic DNA ligation. A 41-nucleotide class 1 deoxyribozyme requires Cu(2+) as a cofactor and adopts a structure that recognizes both the adenine and triphosphate moieties of ATP or dATP. The catalytic efficiency for this DNA, measured at 10(4) M(-1) x min(-1) using either ATP or dATP as substrate, is similar to other catalytic nucleic acids that use small substrates. Chemical probing and site-directed mutagenesis implicate the formation of guanine quartets as critical components of the active structure. The observation of ATP-dependent "self-charging" by DNA suggests that DNA could be made to perform the reactions typically associated with DNA cloning, but without the assistance of protein enzymes.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Li
authors.forename: Y
authors.initials: Y
authors.lastname: Liu
authors.forename: R R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D017122:Bacteriophage T4 / Q000201:enzymology; D001482:Base Composition; D001483:Base Sequence; D002384:Catalysis; D004247:DNA / Q000737:chemistry*; D011088:DNA Ligases / Q000737:chemistry; D021881:DNA, Catalytic; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000145:classification; D011756:Diphosphates / Q000737:chemistry; D006151:Guanosine / Q000737:chemistry; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010428:Pentosephosphates / Q000737:chemistry; D013329:Structure-Activity Relationship
chemical_list: D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D011756:Diphosphates; D010428:Pentosephosphates; D006151:Guanosine; D000255:Adenosine Triphosphate; D004247:DNA; D011088:DNA Ligases