Capping DNA with DNA

Biochemistry. 2000 Mar 21;39(11):3106-14. doi: 10.1021/bi992710r.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Bacteriophage T4 / enzymology
  • Base Composition
  • Base Sequence
  • Catalysis
  • DNA / chemistry*
  • DNA Ligases / chemistry
  • DNA, Catalytic
  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / classification
  • Diphosphates / chemistry
  • Guanosine / chemistry
  • Kinetics
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Pentosephosphates / chemistry
  • Structure-Activity Relationship


  • DNA, Catalytic
  • DNA, Single-Stranded
  • Diphosphates
  • Pentosephosphates
  • Guanosine
  • Adenosine Triphosphate
  • DNA
  • DNA Ligases