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

Hee Kyung Kim, Ivan Rasnik, Juewen Liu, Taekjip Ha, Yi Lu

Research output: Contribution to journalArticlepeer-review

95 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)763-768
Number of pages6
JournalNature chemical biology
Issue number12
StatePublished - Dec 2007
Externally publishedYes

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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