Effects of Bis(aromatic) Pendants on Recognition of Nucleobase Thymine by Zn2+ -1,4,7,10-tetraazacyclododecane (Zn2+ -cyclen)

We have previously shown that the nucleobase thymine binding to Zn²⁺ -cyclen (cyclen=1,4,7,10-tetraazacyclododecane) complex became stronger by appending acridine, naphthalene, or quinoline rings to the cyclen. Amongst these, the pendant bis((1-naphthyl)methyl) or bis((4-quinolyl)methyl) groups yielded the most effective thymine-recognizing Zn²⁺ -cyclen complexes [J. Am. Chem. Soc., 121 (1999) 5426]. The present study was undertaken to find causes of the bis(aromatic) ring effect by X-ray crystal structure analysis and NMR studies. The crystal structure of the Zn²⁺ -bis((1-naphthyl)methyl)-cyclen complex with a deprotonated 1-methylthymine (1-MeT) failed to show the anticipated evidence for the double ~ - ~ stacking interactions between the two naphthalenes and the Zn 2+ -bound 1-MeT m (1-MeT m =N(3')-deprotonated 1-MeT). Crystal data: formula C₃₆ H₄₇ N₇ O₇ Zn, M r =755.19, monoclinic, space group P2₁/ c (No. 14), a =15.438(2) Å, b =14.093(3) Å, c =16.726(2) Å, g =90.53(1) V =3638.7(8) Å 3 Z =4, R =0.035, R _w =0.049. However, the ¹H NMR studies of Zn²⁼ -bis((4-quinolyl)methyl)-cyclen with 1-MeT in varying H₂O/CH₃ CN solution showed increasing upfield shifts of Me(5') and H(6') of the Zn²⁺ -bound 1-MeT in more aqueous media, indicating that the double intercalation with the two quinolines became more significant in more protic environments. We conclude that the double ~ - ~ stacking effect accounts for the enhanced recognition of thymine base by the appended bis((1-naphthyl)methyl) or bis((4-quinolinyl)methyl) groups.     

Fluorescence Energy Transfer Study of Interstrand DNA Cross-linking Caused by Rigid Bisintercalator

The intermolecular cross-linking of DNA with a rigid bisintercalator, 1,4-bis(( N -methylquinolinium-4-yl)vinyl)benzene (pMQVB) has been studied using fluorescence resonance energy transfer (FRET), fluorescence anisotropy measurements, and dynamic fluorescence microscopy. Short DNA duplexes, single-labeled with fluorescein (donor) and x-rhodamine (acceptor), were used as energy transfer partners. Due to the quenching effect of pMQVB on the emission of both fluorescein and x-rhodamine, the energy transfer was monitored using the corrected Stern-Volmer plots. The cross-linking ability of pMQVB depended on the ligand structure; the planar E , E isomer cross-linked DNA contrary to the non-planar E , Z isomer. Dynamic fluorescence microscopy observation also demonstrated the ability of pMQVB to cross-link large T4 DNA molecules.