Dissecting metal ion-dependent folding and catalysis of a single DNAzyme.
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.
Kim
Hee-Kyung
HK
Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Rasnik
Ivan
I
Liu
Juewen
J
Ha
Taekjip
T
Lu
Yi
Y
D001483:Base Sequence; D002384:Catalysis; D021881:DNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D007477:Ions / Q000737:chemistry; D007854:Lead / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D019216:Metals, Heavy / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D017510:Protein Folding; D015032:Zinc / Q000737:chemistry
D021881:DNA, Catalytic; D007477:Ions; D019216:Metals, Heavy; D007854:Lead; D008274:Magnesium; D015032:Zinc