Duplex-Promoted Platination of Adenine-N3 in the Minor Groove of DNA:  Challenging a Longstanding Bioinorganic Paradigm

• Published in: Journal of the American Chemical Society 2005-02, Vol.127 (4), p.1160-1169
• Main Authors: Barry, Colin G, Day, Cynthia S, Bierbach, Ulrich
• Format: Article
• Language: English
• Subjects: Adenine - chemistry; Biological and medical sciences; Chromatography, High Pressure Liquid; Crystallography, X-Ray; DNA - chemistry; DNA - drug effects; DNA Adducts - chemistry; Fundamental and applied biological sciences. Psychology; Interactions. Associations; Intermolecular phenomena; Molecular biophysics; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Organoplatinum Compounds - chemistry; Spectrometry, Mass, Electrospray Ionization; Urea - analogs & derivatives; Urea - chemistry
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja0451620

The interactions of [Pt(en)Cl(ACRAMTU-S)](NO3)2 (PT-ACRAMTU, en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea) with adenine in DNA have been studied using a combination of analytical and high-resolution structural methods. For the first time, a cytotoxic platinum(II) complex has been demonstrated to form adducts in the minor groove of DNA through platination of the adenine-N3 endocyclic nitrogen. An acidic depurination assay was developed that allowed the controlled and selective (pH 2, 60 °C, 12 h) release of platinum-modified adenine from drug-treated nucleic acid samples. From the digested mixtures, three adducts were isolated by semipreparative reverse phase high-performance liquid chromatography and studied by electrospray ionization mass spectrometry (in-line LC−MS), variable-pH 1H NMR spectroscopy, and, where applicable, X-ray crystallography. The three species were identified as the N7 (A*-I), N3 (A*-II), and N1 (A*-III) linkage isomers of [Pt(en)(ACRAMTU-S)(adenine)]3+ (A*). Incubations carried out with the single- and double-stranded model sequences, d(TA)5 and d(TA)15, as well as native DNA indicate that the adduct profiles (A*-I:A*-II:A*-III ratios) are sensitive to the nature of the nucleic acid template. A*-II was found to be a double-strand specific adduct. The crystal structure of this adduct has been determined, providing ultimate evidence for the N3 connectivity of platinum. A*-II crystallizes in the triclinic space group P1̄ in the form of centrosymmetric dimers, {[Pt(en)(ACRAMTU-S)(adenine-N3)]2}6+. The cations are stabilized by a combination of adenine−adenine base pairing (N6···N1 2.945(5) Å) and mutual acridine−adenine base stacking. Tandem mass spectra and 1H chemical shift anomalies indicate that this type of self-association is not merely a crystal packing effect but persists in solution. The monofunctional platination of adenine at its N7, N3, and N1 positions in a significant fraction of adducts breaks a longstanding paradigm in platinum−DNA chemistry, the requirement for nucleophilic attack of guanine-N7 as the principal step in cross-link formation. The biological consequences and potential therapeutic applications of the unique base and groove recognition of PT-ACRAMTU are discussed.