Highly Potent Fluorogenic Ligands for Triplex DNA: 5-Substituted 2-(Naphthalen-2-yl)-4H-Chromen-4-Ones

Area of Science:

• Medicinal Chemistry
• Molecular Biology
• Biochemistry

Background:

• Flavonoids are promising scaffolds for developing triplex DNA ligands due to ease of modification.
• Previous work identified 5-substituted flavonoids with selective triplex DNA binding.
• Expanding the aromatic surface of flavones can enhance triplex-specific ligand potency.

Purpose of the Study:

• To introduce a novel class of highly potent, triplex-specific ligands based on flavone derivatives.
• To investigate the binding affinity and mechanism of these novel ligands with triplex DNA.
• To evaluate the potential applications of these ligands in DNA structure probing and enzyme inhibition.

Main Methods:

• Synthesis of novel 5-substituted 2-(naphthalen-2-yl)-4H-chromen-4-one derivatives.
• UV thermal denaturation studies to assess triplex DNA stabilization.
• Circular dichroism (CD) analysis to evaluate conformational changes in DNA.
• Fluorescent intercalator displacement assays and viscosity measurements to determine binding modes.
• Electrophoretic mobility shift assays and plasmid-based endonuclease inhibition assays to assess functional activity.

Main Results:

• The novel flavone derivatives strongly stabilize triplex DNA, leading to direct dissociation.
• Ligands induce significant conformational changes in triplex DNA compared to duplex DNA.
• Compound 3b exhibits strong blue fluorescence upon binding to triplex DNA, enabling visualization.
• Compound 3b promotes triplex formation at submicromolar concentrations and inhibits DraI endonuclease activity.

Conclusions:

• Novel flavone derivatives are potent and selective ligands for triplex DNA.
• These compounds offer a versatile platform for developing tools to study and manipulate triplex DNA structures.
• Compound 3b serves as a fluorescent probe for triplex DNA and can modulate DNA-protein interactions.