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

Arylamine modification of guanine base at the G₃ position in the NarI sequence (-G₁G₂CG₃CC-) causes a frameshift mutation. Polymerase and ¹⁹F NMR studies have shown that the next flanking base at the 3' position to the G₃ adduct modulates the mutational outcome because of its different conformations. Here, we have studied the interaction of the 16-mer NarI sequence (5'-CTCTCG₁G₂CCXATCAC-3') (G₃ = N-acetyl-2-aminofluorene (AAF)-dG and X is either C or T) with [Ru(phen)₂(dppz)]²⁺ (phen = 1,10-phenanthroline and dppz = dipyrido[3,2-a:2',3'-c]phenazine). Interaction studies between isomers of Ru(II) and two oligonucleotide models, viz., (a) full duplex, and (b) slipped mutagenic intermediate (SMI), have been carried out. Luminescence studies reveal that the sensitivity of Ru(II) with an adduct increases 2- to 3-fold compared to that of control in full duplex. In SMI, the sensitivity of Ru(II) varies with the next flanking base and in the order of -G^AAFCC > -G^AAFCT. Microscale thermophoretic data reveal that in full duplex Λ-Ru binds to -G^AAFCT- by 13- and 4-fold stronger than its control and -G^AAFCC-, respectively. In SMI, Δ-Ru binds to -G^AAFCC- (41% stacked (S) conformer) by 3-fold while -G^AAFCT- (86% major groove (B) conformer) weakens the binding of Λ-Ru by 250-fold compared to the control. The results presented here reveal that the binding of Ru(II) not only depends on conformations of the AAF-dG adduct but also is isomer-centric and might be helpful in determining the conformational heterogeneity of other covalent aryl/heterocyclic amine-DNA adducts.