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DNA-Catalyzed DNA Cleavage by a Radical Pathway with Well-Defined Products
Yujeong Lee1, Paul C Klauser1, Benjamin M Brandsen1
1Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
Journal of the American Chemical Society
|December 10, 2016
Summary
This study reveals a novel DNA-catalyzed DNA cleavage mechanism using radical pathways. Two new DNA enzymes (deoxyribozymes) excise guanosine nucleosides, producing specific byproducts without requiring redox-active metals.
Area of Science:
- Biochemistry
- Molecular Biology
- Catalysis
Background:
- DNA enzymes (deoxyribozymes) can catalyze various reactions.
- Radical-based DNA cleavage is known but often requires specific conditions and metals.
Purpose of the Study:
- To identify and characterize novel DNA enzymes capable of DNA cleavage.
- To elucidate the mechanism of a DNA-catalyzed radical DNA cleavage process.
Main Methods:
- In vitro selection from random DNA pools to identify deoxyribozymes.
- Mass spectrometry and colorimetric assays for product identification.
- Investigating the role of metal ions, glutathione, superoxide, and hydrogen peroxide.
Main Results:
- Two new deoxyribozymes were discovered that cleave single-stranded DNA.
- A radical-based pathway excises guanosine nucleosides, producing 3'-phosphoglycolate, 5'-phosphate, and base propenal.
- Catalysis is suppressed by glutathione and enhanced by superoxide and hydrogen peroxide; requires only redox-inactive metal ions.
Conclusions:
- A unique DNA-catalyzed radical DNA cleavage mechanism has been identified.
- The deoxyribozymes mimic bleomycin's cleavage products via a C4' radical intermediate.
- This process offers a novel DNA-based approach to DNA cleavage distinct from metal-dependent reactions.
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