title: Small, highly active DNAs that hydrolyze DNA.
abstract: DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (k(obs)) of ~1 min(-1) when incubated near neutral pH in the presence of Zn(2+). Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn(2+), pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Hongzhou
authors.initials: H
authors.lastname: Gu
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Furukawa
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Berenson
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D021881:DNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019020:Directed Molecular Evolution / Q000379:methods; D006868:Hydrolysis; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D015032:Zinc / Q000378:metabolism
chemical_list: D021881:DNA, Catalytic; D004247:DNA; D015032:Zinc