Structural consequences of a 3′ → 3′ DNA interstrand cross-link by a trinuclear platinum complex: unique formation of two such cross-links in a 10-mer duplex

Abstract

Combined multidimensional nuclear magnetic resonance spectroscopy and electrospray mass spectrometry was used to analyze the platinated DNA adduct of the phase II anticancer drug [{trans-PtCl(NH 3 ) 2 } 2 -μ-{trans-Pt(NH 3 ) 2 (NH 2 (CH 2 ) 6 NH 2 ) 2 }](NO 3 ) 4 (BBR3464) with [5′-d (ACG*TATACG*T)-3′] 2 . Two 1,2-interstrand cross-links were formed by concomitant binding of two trinuclear moieties to the oligonucleotide. The four DNA-bound platinum atoms coordinated in the major groove at N7 positions of guanines in the 3′ → 3′ direction and the central platinum unit is expected to lie in the DNA minor groove. This is the first report of such a DNA lesion. The melting temperature of the adduct is 76 °C and is 42 °C higher than that of the unplatinated DNA. The sugar residues of the platinated bases are in the N-type conformation and the G9 nucleoside is in the syn orientation, while the G3 nucleoside appears to retain the anti configuration. The secondary structure of DNA was significantly changed upon cross-linking of the two BBR3464 molecules. Base destacking occurs between A1/C2 and C2/G3 and weakened stacking is seen for the C8/G9 and G9/ T10 bases. The lack of Watson-Crick base pairing is also seen for A1-T10 and C2-G9 base pairs, whereas Watson-Crick base pairs in the central sequence of the DNA (T4 → A7) are well maintained. While DNA repair proteins may "see" different platinated adducts as bulky "lesions", the subtle differences involved in base pairing and stacking, as summarized here, may extend to their role as a substrate for repair enzymes. Thus, differences in protein recognition and repair efficiency among the various interstrand cross-links are likely and a subject worthy of detailed exploration.

Excursions in polynuclear platinum DNA binding

“…The sequence actually allows competition between a 1,2-IXL and a 1,6-IXL to be studied. NMR analysis suggested a structure composed of two simultaneous 1,2-interstrand crosslinks between the adjacent guanines, the first examples therefore of a structurally characterized 3′ → 3′ adduct 40. Relatively large chemical shifts of the H6 and H1′ protons of the corresponding C2 and C8 cytosines as well as the thymidine T4 and T10 bases indicated that guanine platination interrupted base pairing and stacking.…”

Cellular and biomolecular responses of human ovarian cancer cells to cytostatic dinuclear platinum(II) complexes

“…Polynuclear platinum complexes constitute a novel class of prospective anticancer agents that have shown some peculiar activities as compared with mononuclear platinum compounds [4,5]. Unlike cisplatin and its analogues that predominantly form 1,2-d(GpG) and 1,2-d(ApG) intrastrand crosslinks with DNA [6], polynuclear platinum complexes mainly form long range intra-and interstrand crosslinks [4,7]. The Pt-DNA crosslinks can simulate a series of intracellular responses and lead to the death of cancer cells [6].…”

Competitive formation of both long-range 5′–5′ and short-range antiparallel 3′–3′ DNA interstrand cross-links by a trinuclear platinum complex on binding to a 10-mer duplex

“…7 Reaction of Triplatin with the DNA duplex 5´–{d(ACGTATACGT) 2 } (duplex I , Chart 1) resulted in formation of two simultaneous 3´–3´ 1,2–GG IXLs. 14 The structure as analyzed by 2D NMR spectroscopy (NOESY, COSY, TOCSY) is quite distinct from the analogous cisplatin 1,2-interstrand (GC) 2 adduct where the cytosines of the G-C base pairs are “flipped out” of the helix upon G-platination. 15 Duplex I offers the possibility for the competitive formation of both 3´–3´ 1,2–GG and a 5´–5´ 1,6–GG IXLs and we have previously shown (using 2D [ 1 H, 15 N] HSQC NMR spectroscopy) that Triplatin forms a 5´–5´ 1,6–GG IXL in the DNA duplex 5´–d{TATGTATACATA} 2 (duplex II ).…”

“…15 Duplex I offers the possibility for the competitive formation of both 3´–3´ 1,2–GG and a 5´–5´ 1,6–GG IXLs and we have previously shown (using 2D [ 1 H, 15 N] HSQC NMR spectroscopy) that Triplatin forms a 5´–5´ 1,6–GG IXL in the DNA duplex 5´–d{TATGTATACATA} 2 (duplex II ). 5 Since duplex I offers the possibility for this cross-link to form, the minor product observed by ESI-MS in the study of its reaction with Triplatin 14 may indeed be the 1,6-cross-link formed as a result of rearrangement of the adducts under the experimental conditions. Herein we have used 1D 1 H and 2D [ 1 H, 15 N] HSQC NMR spectroscopy to follow the stepwise formation of interstrand cross-links by reaction of 15 N–Triplatin ( 15 N- 1 ) with duplex I and to compare with the observed structural features of the isolated adduct.…”