ArticleNucleic acids research2004
Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 77 citations in OpenAlex.
- Dynamism and evolvability in nucleic acid enzymes.Nature communications · 2026Article
- Programming DNA machines to move.Nature reviews. Chemistry · 2026Review
- A minimal RNA-cleaving DNAzyme and its catalytic mechanism.Nucleic acids research · 2026Article
- The Programmable Catalytic Core of 8-17 DNAzymes.Molecules (Basel, Switzerland) · 2024Article
- Development of a DNAzyme Walker for the Detection of APE1 in Living Cancer Cells.Analytical chemistry · 2023Article
- A Semisynthetic Bioluminescence Sensor for Ratiometric Imaging of Metal Ions In Vivo Using DNAzymes Conjugated to An Engineered Nano-Luciferase.Angewandte Chemie (International ed. in English) · 2023Article
- Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.Biochemistry · 2023Article
- Single-Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics.International journal of molecular sciences · 2023Article
- DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells.Angewandte Chemie (International ed. in English) · 2020Article
- DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells.Angewandte Chemie (Weinheim an der Bergstrasse, Germany) · 2020Article
- Nucleic Acid Catalysis under Potential Prebiotic Conditions.Chemistry, an Asian journal · 2020Review
- Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.Nucleic acids research · 2019Article
- Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme.Biochemistry · 2018Article
- Isolation of DNA aptamers for herbicides under varying divalent metal ion concentrations.Aptamers (Oxford, England) · 2018Article
- DNA Catalysis: The Chemical Repertoire of DNAzymes.Molecules (Basel, Switzerland) · 2015Review
- Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.PloS one · 2014Article
- Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: a uranyl photocleavage study.Nucleic acids research · 2013Article
- Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods.Nucleic acids research · 2011Article
- On the curvature in logarithmic plots of rate coefficients for chemical reactions.Chemistry Central journal · 2011Article
- DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli.BMC biotechnology · 2010Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 8-17 deoxyribozyme is a small DNA catalyst of significant applicative interest. We have analyzed the kinetic features of a well behaved 8-17 construct and determined the influence of several reaction conditions on such features, providing a basis for further exploration of the deoxyribozyme mechanism. The 8-17 bound its substrate with a rate constant approximately 10-fold lower than those typical for the annealing of short complementary oligonucleotides. The observed free energy of substrate binding indicates that an energetic penalty near to +7 kcal/mol is attributable to the deoxyribozyme core. Substrate cleavage required divalent metal ion cofactors, and the dependence of activity on the concentration of Mg2+, Ca2+ or Mn2+ suggests the occurrence of a single, low-specificity binding site for activating ions. The efficiency of activation correlated with the Lewis acidity of the ion cofactor, compatible with a metal-assisted deprotonation of the reactive 2'-hydroxyl group. However, alternative roles of the metal ions cannot be excluded, because those ions that are stronger Lewis acids are also capable of forming stronger interactions with ligands such as the phosphate oxygens. The apparent enthalpy of activation for the 8-17 reaction was close to the values observed for hydroxide-catalyzed and hammerhead ribozyme-catalyzed RNA cleavage.
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