Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes

Chem Biol. 2002 Apr;9(4):507-17. doi: 10.1016/s1074-5521(02)00127-8.


Although DNA has not been found responsible for biological catalysis, many artificial DNA enzymes have been created by "in vitro selection." Here we describe a new selection approach to assess the influence of four common divalent metal ions (Ca(2+), Cu(2+), Mg(2+), and Mn(2+)) on sequence diversity, metal specificity, and catalytic proficiency of self-phosphorylating deoxyribozymes. Numerous autocatalytic DNA sequences were isolated, a majority of which were selected using Cu(2+) or Mn(2+) as the divalent metal cofactor. We found that Cu(2+)- and Mn(2+)-derived deoxyribozymes were strictly metal specific, while those selected by Ca(2+) and Mg(2+) were less specific. Further optimization by in vitro evolution resulted in a Mn(2+)-dependent deoxyribozyme with a k(cat) of 2.8 min(-1). Our findings suggest that DNA has sufficient structural diversity to facilitate efficient catalysis using a broad scope of metal cofactor utilizing mechanisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence*
  • Calcium / metabolism
  • Calcium / pharmacology
  • Catalysis / drug effects
  • Cations, Divalent / metabolism
  • Cations, Divalent / pharmacology
  • Copper / metabolism
  • Copper / pharmacology
  • DNA, Catalytic / chemistry
  • DNA, Catalytic / genetics
  • DNA, Catalytic / metabolism*
  • Kinetics
  • Magnesium / metabolism
  • Magnesium / pharmacology
  • Manganese / metabolism
  • Manganese / pharmacology
  • Metals, Heavy / metabolism*
  • Metals, Heavy / pharmacology
  • Molecular Sequence Data
  • Phosphorylation / drug effects


  • Cations, Divalent
  • DNA, Catalytic
  • Metals, Heavy
  • Manganese
  • Copper
  • Magnesium
  • Calcium