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

Although DNA has not been found responsible for biological catalysis, many artificial DIVA 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 (Ca2+, Cu2+, Mg2+, and Mn2+) 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 Cu2+ or Mn2+ as the divalent metal cofactor. We found that Cu2+- and Mn2+-derived deoxyribozymes were strictly metal specific, while those selected by Ca2+ and Mg2+ were less specific. Further optimization by in vitro evolution resulted in a Mn2+-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.