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Updated: Aug 22, 2025
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
Published on: April 4, 2025
G-quadruplex-containing oligodeoxynucleotides as DNA topoisomerase I inhibitors
Dawei Li1, Xiyu Chen1, Rumeng Yan2
1Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
Abstract:
DNA topoisomerase I was found to be highly abundant in fast-proliferating tumor cells and is a potential target for anticancer therapy. A series of G-quadruplex-containing oligodeoxynucleotides (ODNs) were designed and used as inhibitors of DNA topoisomerase I. It was demonstrated that ODNs with G-quadruplexes can efficiently inhibit the supercoiled DNA relaxation reaction catalyzed by DNA topoisomerase I. Compared with the other conformations, the parallel propeller-type G-quadruplex was the most efficient DNA topoisomerase I inhibitor. Further studies revealed that integrating G-quadruplexes with duplexes to form quadruplex-duplex hybrids could significantly improve the inhibition efficiency. In addition, a circular ODN that consists of a G-quadruplex motif and DNA topoisomerase I binding site was synthesized and used as a DNA topoisomerase I inhibitor. The results showed that the particularly designed circular ODN displayed high inhibitory efficiency on the activity of DNA topoisomerase I with an IC50 value of 54.8 nM. Moreover, the circular ODN exhibited excellent thermal stability and nuclease resistance. Considering the low cytotoxicity of DNA-based biopharmaceuticals, the design strategy and results reported in this study may shed new light on nucleic acid-based DNA topoisomerase I inhibitor construction for potential anticancer drugs.
Insights
Novel DNA structures, specifically G-quadruplexes within oligodeoxynucleotides (ODNs), show potent inhibition of DNA topoisomerase I. A circular ODN demonstrated high efficiency and stability, offering a promising strategy for anticancer drug development.
Area of Science:
- Biochemistry
- Molecular Biology
- Medicinal Chemistry
Background:
- DNA topoisomerase I is highly abundant in rapidly proliferating tumor cells.
- This enzyme is a validated target for anticancer therapeutic strategies.
Purpose of the Study:
- To design and evaluate G-quadruplex-containing oligodeoxynucleotides (ODNs) as inhibitors of DNA topoisomerase I.
- To explore structural modifications for enhanced inhibitory efficiency.
Main Methods:
- Synthesis of various G-quadruplex-containing ODNs, including quadruplex-duplex hybrids and a circular ODN.
- Assay of DNA topoisomerase I activity inhibition using supercoiled DNA relaxation assays.
- Evaluation of thermal stability and nuclease resistance of the designed ODNs.
Main Results:
- ODNs with G-quadruplexes effectively inhibited DNA topoisomerase I activity.
- Parallel propeller-type G-quadruplexes exhibited the highest inhibitory efficiency.
- Quadruplex-duplex hybrids and a specifically designed circular ODN significantly enhanced inhibition, with the circular ODN showing an IC50 of 54.8 nM.
- The circular ODN demonstrated excellent thermal stability and resistance to nucleases.
Conclusions:
- G-quadruplex-containing ODNs, particularly circular constructs, are potent inhibitors of DNA topoisomerase I.
- This strategy offers a promising avenue for developing novel nucleic acid-based anticancer drugs with potentially low cytotoxicity.
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