NMR AND MOLECULAR MODELING STUDIES OF THE INTERACTION OF ARTIFICIAL AP LYASES WITH A DNA DUPLEX CONTAINING AN APURINIC ABASIC SITE MODEL

Tailor-made molecules, DTAc and ATAc, that incorporate a nucleic base (adenine or 2,6-diaminopurine) linked by a diamino chain to an interca lator (9-amino-6-chloro-2-methoxyacridine) selectively recognize and e fficiently cleave abasic sites in DNA via a p-elimination reaction. Th e threedimensional structure of the complexes of DTAc and ATAc bound t o a DNA undecamer, the G(20)T(19)G(18)T(17)G(16)T(15)G(14)C(13)G(12))( 5') duplex in which the X residue is a stable abasic site [3-hydroxy-2 -(hydroxymethyl)tetrahydrofuran], has been studied by combined NMR-ene rgy minimization methods. Analysis of the NMR spectra reveals that DTA c and ATAc interact with a very similar fashion and form two different complexes with DNA, present in a ratio of 70/30 (+/-10). In both comp lexes, the acridine ring intercalates exclusively between the C3.G20 a nd A4.T19 base pairs, the linker is located in the minor groove, and t he base moiety docks in the abasic site. The principal difference betw een the major and the minor complexes consists of a 180 degrees rotati on of the acridine ring around the Acr-C-N bond within the same interc alation site. Molecular modeling studies with few intermolecular ligan d-DNA restraints were used to investigate the geometry of the base pai r formed between the diaminopurine of DTAc and the T17 ring. The most energetically favored complex has the 2,6-diaminopurine of DTAc base p aired with the T17 ring in a Hoogsteen conformation. The models DTAc a nd ATAc are also discussed as nuclease mimics and cleaving agents at a basic sites.