Dissecting metal ion-dependent folding and catalysis of a single DNAzyme

Nat Chem Biol. 2007 Dec;3(12):763-8. doi: 10.1038/nchembio.2007.45. Epub 2007 Oct 28.


Protein metalloenzymes use various modes for functions for which metal-dependent global conformational change is required in some cases but not in others. In contrast, most ribozymes require a global folding that almost always precedes enzyme reactions. Herein we studied metal-dependent folding and cleavage activity of the 8-17 DNAzyme using single-molecule fluorescence resonance energy transfer. Addition of Zn2+ and Mg2+ induced folding of the DNAzyme into a more compact structure followed by a cleavage reaction, which suggests that the DNAzyme may require metal-dependent global folding for activation. In the presence of Pb2+, however, the cleavage reaction occurred without a precedent folding step, which suggests that the DNAzyme may be prearranged to accept Pb2+ for the activity. Neither ligation reaction of the cleaved substrates nor dynamic changes between folded and unfolded states was observed. These features may contribute to the unusually fast Pb2+-dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use.

Publication types

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

MeSH terms

  • Base Sequence
  • Catalysis
  • DNA, Catalytic / chemistry*
  • DNA, Catalytic / metabolism*
  • Ions / chemistry
  • Lead / chemistry
  • Magnesium / chemistry
  • Metals, Heavy / chemistry*
  • Nucleic Acid Conformation
  • Protein Folding*
  • Zinc / chemistry


  • DNA, Catalytic
  • Ions
  • Metals, Heavy
  • Lead
  • Magnesium
  • Zinc