Nucleic Acids Research, Vol 26, Issue 14 3385-3391, Copyright © 1998 by Oxford University Press
N Ota, M Warashina, K Hirano, K Hatanaka and K Taira
As a part of our efforts to clarify structure-function relationships in
reactions catalyzed by deoxyribozymes (DNAzymes), which were recently
selected in vitro , we synthesized various chimeras and analyzed the
kinetics of the corresponding cleavage reactions. We focused on the binding
arms and generated helices composed of binding arms and substrates that
consisted of RNA and RNA, of RNA and DNA or of DNA and DNA. As expected for
the rate limiting chemical cleavage step in reactions catalyzed by
DNAzymes, a linear relationship between log( k cat) and pH was observed. In
all cases examined, introduction of DNA into the binding helix enhanced the
rate of chemical cleavage. Comparison of CD spectra of DNAzyme. substrate
complexes suggested that higher levels of B-form-like helix were associated
with higher rates of cleavage of the substrate within the complex. To our
surprise, the enhancement of catalytic activity that followed introduction
of DNA into the binding helix (enhancement by the presence of more
B-form-like helix) was very similar to that observed in the case of the
hammerhead ribozymes that we had investigated previously. These data,
together with other observations, strongly suggest that the reaction
mechanism of metal-ion-dependent DNAzymes is almost identical to that of
hammerhead ribozymes.
ARTICLES
Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity
National Institute for Advanced Interdisciplinary Research, Agency of Industrial Science and Technology, MITI, Tsukuba Science City 305-8562, Japan.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. Schlosser and Y. Li DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides Nucleic Acids Res., February 1, 2009; 37(2): 413 - 420. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. K. Silverman In vitro selection, characterization, and application of deoxyribozymes that cleave RNA Nucleic Acids Res., November 11, 2005; 33(19): 6151 - 6163. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-K. Cheong, E. Hwang, C. Lee, B.-S. Choi, and C. Cheong Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography Nucleic Acids Res., June 15, 2004; 32(10): e84 - e84. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Chen, R. Wang, Z. Li, B. Liu, X. Wang, Y. Sun, D. Hao, and J. Zhang A novel replicating circular DNAzyme Nucleic Acids Res., April 28, 2004; 32(8): 2336 - 2341. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Bonaccio, A. Credali, and A. Peracchi Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme Nucleic Acids Res., February 12, 2004; 32(3): 916 - 925. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Cieslak, J. Szymanski, R. W. Adamiak, and C. S. Cierniewski Structural Rearrangements of the 10-23 DNAzyme to {beta}3 Integrin Subunit mRNA Induced by Cations and Their Relations to the Catalytic Activity J. Biol. Chem., November 28, 2003; 278(48): 47987 - 47996. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Schubert, D. C. Gul, H.-P. Grunert, H. Zeichhardt, V. A. Erdmann, and J. Kurreck RNA cleaving '10-23' DNAzymes with enhanced stability and activity Nucleic Acids Res., October 15, 2003; 31(20): 5982 - 5992. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Levy and A. D. Ellington Exponential growth by cross-catalytic cleavage of deoxyribozymogens PNAS, May 27, 2003; 100(11): 6416 - 6421. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Q. Sun, M. J. Cairns, E. G. Saravolac, A. Baker, and W. L. Gerlach Catalytic Nucleic Acids: From Lab to Applications Pharmacol. Rev., September 1, 2000; 52(3): 325 - 348. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Cairns, A. King, and L.-Q. Sun Nucleic acid mutation analysis using catalytic DNA Nucleic Acids Res., February 1, 2000; 28(3): e9 - e9. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Li, W. Zheng, A. H. Kwon, and Y. Lu In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme Nucleic Acids Res., January 15, 2000; 28(2): 481 - 488. [Abstract] [Full Text] [PDF]
|
|