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Updated: Oct 5, 2025
05:37
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
Published on: April 4, 2025
877
A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability
Elaina P Boyle1,2, Levan Lomidze3, Karin Musier-Forsyth1,2
1Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
Chemistryopen
|February 1, 2022
Summary
Nucleic acid quadruplexes, like the thrombin-binding aptamer (TBA), can be stabilized by specific DNA→RNA substitutions. This research enhances TBA stability, offering potential for advanced nanomachines and biotechnological applications.
Area of Science:
- Biochemistry
- Molecular Biology
- Biotechnology
Background:
- Nucleic acid quadruplexes regulate gene expression and are key components in aptamers for binding applications.
- Understanding quadruplex structure and stability is crucial for their use in medicine and biotechnology.
- The thrombin-binding aptamer (TBA) is a well-studied monomolecular, antiparallel quadruplex.
Purpose of the Study:
- To evaluate the impact of DNA→RNA substitutions on the stability and topology of the thrombin-binding aptamer (TBA).
- To identify specific substitution patterns that enhance quadruplex stability for potential applications.
Main Methods:
- Investigated DNA→RNA substitutions (G→g) within the TBA sequence in the presence of K+ or Sr2+.
- Analyzed changes in quadruplex structure and thermodynamic properties.
- Designed and tested a chimeric DNA/RNA TBA construct.
Main Results:
- Substitutions at syn G residues destabilized the quadruplex, while substitutions at anti G residues enhanced stability without altering topology.
- Loop position substitutions had varied and unpredictable effects on stability but did not change the quadruplex topology.
- A chimeric DNA/RNA TBA construct exhibited significantly improved stability compared to the all-DNA TBA.
Conclusions:
- Specific DNA→RNA substitutions can be strategically employed to enhance the stability of nucleic acid quadruplexes.
- The findings provide a basis for designing more stable quadruplex structures for diverse applications, including nanomachines.
- This work has implications for advancing aptamer-based technologies and therapeutic strategies.
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