Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions

Debapriya Mazumdar, Nandini Nagraj, Hee Kyung Kim, Xiangli Meng, Andrea K. Brown, Qian Sun, Wei Li, Yi Lu

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The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K +, Rb +, or Cs + or in the presence of 80 mM, [Co(NH 3) 6] 3+. Only 4 M Li +, NH 4 + and, to a lesser extent, Na + conferred detectable activity. The observed rate constants (k obs ≈ 10 -3 min -1 for Li + and NH 4 +) are ∼1000-fold lower than that in the presence of 10 mM Mg 2+, and ∼200,000-fold slower than that in the presence of 100 μM Pb 2+. Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within ∼10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb 2+ sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K d ∼ 0.35 M for Rb + and Cs +), while those that confer DNAzyme activity possess stronger affinity (K d ∼ 0.22 M for Li +, Na + and NH 4 +). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb 2+; higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn 2+ and Mg 2+; the K d values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb 2+. These results indicate that Pb 2+-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.

Original languageEnglish (US)
Pages (from-to)5506-5515
Number of pages10
JournalJournal of the American Chemical Society
Issue number15
StatePublished - Apr 22 2009

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry


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