Selective Recognition of Conformation-Specific Arylamine-DNA Adduct in Frameshift Model by [Ru(phen)₂(dppz)]²

Area of Science:

• DNA adducts
• Chemical carcinogenesis
• Coordination chemistry

Background:

• Arylamine modification of guanine bases, specifically at the G3 position within the NarI sequence, induces frameshift mutations.
• The conformational flexibility of the DNA adduct and its flanking bases significantly influences the mutagenic outcome.
• Ruthenium(II) polypyridyl complexes, such as [Ru(phen)2(dppz)]2+, are utilized as probes to investigate DNA-adduct interactions.

Purpose of the Study:

• To investigate the interaction of a specific 16-mer NarI DNA sequence containing an N-acetyl-2-aminofluorene (AAF)-dG adduct with [Ru(phen)2(dppz)]2+ isomers.
• To compare the binding of ruthenium complexes to both the full duplex and the slipped mutagenic intermediate (SMI) forms of the DNA.
• To elucidate how the conformation of the AAF-dG adduct and its 3'-flanking base (cytosine or thymine) affect ruthenium complex binding.

Main Methods:

• Synthesis and characterization of oligonucleotide models containing the AAF-dG adduct.
• Luminescence spectroscopy to study the interaction of ruthenium complexes with DNA models.
• Microscale thermophoresis (MST) to quantify binding affinities and thermodynamics.
• Conformational analysis of DNA adducts and intermediates.

Main Results:

• Ruthenium complex luminescence sensitivity increased 2-3 fold upon binding to the AAF-dG adduct in the full duplex DNA.
• In the slipped mutagenic intermediate (SMI), ruthenium sensitivity varied with the 3'-flanking base, showing higher sensitivity for -GAAF-CC- than -GAAF-CT-.
• Microscale thermophoresis revealed differential binding affinities: Lambda-Ru bound -GAAF-CT- 13-fold stronger than its control in duplex DNA, while Delta-Ru binding to -GAAF-CC- in SMI was 3-fold stronger, and binding to -GAAF-CT- weakened Lambda-Ru binding by 250-fold.

Conclusions:

• Ruthenium(II) complex binding to AAF-dG adducts is dependent on the adduct's conformation and the isomer of the ruthenium complex.
• The conformational heterogeneity of aryl/heterocyclic amine-DNA adducts can be probed using ruthenium complexes.
• This study provides insights into the isomer-specific recognition of conformationally distinct DNA adducts, relevant for understanding mutagenesis and developing diagnostic tools.