ArticleNucleic acids research1998
Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity.
Article in Nucleic acids research, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 57 citations in OpenAlex.
- Multicomponent nucleic acid enzymes as signal amplification strategy for the detection of microRNA based on fluorescence resonance energy transfer.Mikrochimica acta · 2025Article
- DNA Catalysis: Design, Function, and Optimization.Molecules (Basel, Switzerland) · 2024Review
- Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme.International journal of molecular sciences · 2023Article
- Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes.Inorganica chimica acta · 2016Article
- Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme.Journal of biosciences · 2012Article
- Article
- MNAzymes, a versatile new class of nucleic acid enzymes that can function as biosensors and molecular switches.Journal of the American Chemical Society · 2010Article
- Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions.Journal of the American Chemical Society · 2009Article
- DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides.Nucleic acids research · 2009Article
- Systematic analysis of the role of target site accessibility in the activity of DNA enzymes.Journal of RNAi and gene silencing : an international journal of RNA and gene targeting research · 2006Article
- Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets.BMC molecular biology · 2006Article
- Design of efficient DNAzymes against muscle AChR alpha-subunit cRNA in vitro and in HEK 293 cells.Journal of RNAi and gene silencing : an international journal of RNA and gene targeting research · 2005Article
- In vitro selection, characterization, and application of deoxyribozymes that cleave RNA.Nucleic acids research · 2005Review
- Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography.Nucleic acids research · 2004Article
- A novel replicating circular DNAzyme.Nucleic acids research · 2004Article
- Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme.Nucleic acids research · 2004Article
- RNA cleaving '10-23' DNAzymes with enhanced stability and activity.Nucleic acids research · 2003Article
- Exponential growth by cross-catalytic cleavage of deoxyribozymogens.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Nucleic acid mutation analysis using catalytic DNA.Nucleic acids research · 2000Article
- In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme.Nucleic acids research · 2000Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.