Elaboration of Selective and Efficient Recognition of Thymine Base in Dinucleotides (TpT, ApT, CpT, and GpT), Single-Stranded d(GTGACGCC), and Double-Stranded d(CGCTAGCG)₂ by Zn²⁺−Acridinylcyclen (Acridinylcyclen = (9-Acridinyl)methyl-1,4,7,10-tetraazacyclododecane)

Previously, we reported that the Zn2+−acridinylcyclen complex (ZnL‘, acridinylcyclen = (9-acridinyl)methyl-1,4,7,10-tetraazacyclododecane) strongly recognizes thymine base (T) in thymidine nucleoside and weakly guanine (G) in 2‘-deoxyguanosine in aqueous solution (Shionoya and Kimura et al. J. Am. Chem. Soc. 1993, 115, 6730−6737; J. Am. Chem. Soc. 1994, 116, 3848−3859). In this paper, we elaborate on the ZnL‘ recognition of T in dinucleotides (thymidylylthymidine (TpT), 2‘-deoxyguanylylthymidine (GpT), 2‘-deoxycytidylylthymidine (CpT), and 2‘-deoxyadenylylthymidine (ApT)) and octanucleotides (single-stranded d(GTGACGCC) and double-stranded d(CGCTAGCG)2) by means of UV spectrophotometric titration, potentiometric pH titration, 1H NMR, FAB-MS measurements, and molecular modeling. The primary mode of interaction of ZnL‘ with the deprotonated thymine bases (T-) in all of these oligonucleotides was prevalent with the common affinity constants Kapp of ca. 105 M-1 (Kapp = [T--bound ZnL‘]/[uncomplexed ZnL‘] [uncomplexed oligonucleotide]) at pH 8 and 25 °C with I = 0.10 (NaNO3) regardless of the adjacent bases. The secondary mode involving π−π stacking between two acridines made the synergistic binding of the two ZnL‘ complexes with TpT. Thus, the second ZnL‘ interaction with TpT was about 20 times more favored than the first one. The subsequent interaction of ZnL‘ with G occurred to the ZnL‘-bound GpT- and d(GT-GACGCC). The NMR study showed the double-strand destabilization of d(CGCTAGCG)2 by formation of the ZnL‘−T- complex.