A Rare Example of Three Abundant Conformers in One Retro Model of the Cisplatin−DNA d(GpG) Intrastrand Cross Link. Unambiguous Evidence That Guanine O6 to Carrier Amine Ligand Hydrogen Bonding Is Not Important. Possible Effect of the Lippard Base Pair Step Adjacent to the Lesion on Carrier Ligand Hydrogen Bonding in DNA Adducts

Abstract

Guanine O6 to carrier ligand hydrogen bonding is a central feature of many hypotheses advanced to explain the anticancer activity of cis-type anticancer drugs, cis-PtA(2)X(2) (A(2) = diamine or two amines). Early structural evidence suggested that cis-Pt(NH(3))(2)(d(GpG)) (the cross-link model for the key cisplatin-DNA adduct) and other cis-PtA(2)(d(GpG)) adducts exist exclusively or mainly as the HH1 conformer with head-to-head (HH) bases. The dynamic motion of the d(GpG) in these adducts is too rapid to permit definitive characterization of both the conformation and the H-bonding. Hence, we use retro models having A(2) ligands designed to slow the motion. Here, we employ Me(2)ppz (N,N'-dimethylpiperazine), which lacks NH groups. Me(2)ppz is unique in having sp(3) N-methyl groups directly in the coordination plane, allowing the coexistence of multiple conformers but hindering dynamic motion in Me(2)ppzPt(d(GpG)) and Me(2)ppzPt(GpG) retro models. Dynamic processes are decreased enough in Me(2)ppzPt(d(GpG)) to permit HPLC separation of three abundant forms. After HPLC separation, the three re-equilibrate, proving that the three forms must be conformers and that Me(2)ppz has little influence on conformer distribution. This marks the first reported characterization of three abundant conformers for one cis-PtA(2)(d(GpG)) adduct. From NMR evidence, the Me(2)ppzPt(d(GpG)) HH1 conformer has uncanted bases. Another conformer, one of two recently discovered conformer types, has head-to-tail (HT) bases with Delta chirality. For this Delta HT1 form, several lines of evidence establish that the dinucleotide moieties have essentially identical structures in d(GpG) (and GpG) adducts of Me(2)ppzPt and other cis-PtA(2) complexes. For example, the shifts of the highly structure-sensitive G H8 NMR signals are almost identical for the Delta HT1 form of all adducts. In previous models, the stabilization of the Delta HT1 form could be attributed to G O6 H-bonding to A(2) NH groups. Such H-bonds are not possible for Me(2)ppz. The unambiguous conclusions are that G O6 H-bonding is weak and that neither canting nor H-bonding is essential in HH forms. These two features are present in almost all other small models but are essentially absent in the cross-link base pair (bp) step in duplexes. We conclude from our work that the forces favoring canting and H-bonding are weak, and we hypothesize that steric effects within the Lippard bp step adjacent to this cross-link bp step easily overcome these forces.

Cisplatin Adducts on a GGG Sequence within a DNA Duplex Studied by NMR Spectroscopy and Molecular Dynamics Simulations

“…The influence of such hydrogen bonding on the structure of the adduct and its eventual role in anticancer activity has been a recurrent issue of debate (refs. [4,29,44,45], and references therein). In the crystal structure of a cisplatin-bound DNA dodecamer, for instance, the 5'-oriented NH 3 ligand is hydrogen-bonded to the phosphodiester group at the 5'-side.…”

2.4-Å Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex

“…The crystallographic studies from our laboratory and computational studies by Marzilli and co-workers (34,35) have demonstrated that platinum-DNA adducts are nearly structurally homologous, even in the minor groove where most protein-DNA interactions occur. Yet these proteins are able to recognize differentially adducts that contain differing amine ligands (16), and platinum complexes with different spectator ligands inhibit transcription to varying degrees (37).…”

“…Recent work by the Marzilli group (34,35) suggested that hydrogen bonding between platinated guanine bases and their associated phosphate groups with the ammine or amine ligands in a {PtL 2 } 2ϩ complex (L 2 is two amines or a diamine) is extremely weak. In the present 3Ј orientational isomer, the hydrogen bond with O-6 of the 3Ј guanine is quite substantial and, in our previous {Pt(dach)} 2ϩ complex, there was a similarly strong hydrogen bond on the 3Ј-end involving the amino group of dach and the 3Ј-phosphate.…”

DNA fragment conformations in adducts with Kiteplatin

“…In this case there is quite an intense H8-H1′ crosspeak. The presence of a H8-H1′ cross-peak indicates either a partial syn character [58][59][60]64,91,94 for the 3′-G of the dominant conformer or, more likely, the existence of a minor ΔHT1 conformer in dynamic equilibrium with the dominant HH1 conformer. Such a dynamic equilibrium would explain the somewhat broad nature of the H8 signals, even at −5°C (Fig.…”

“…For the ΔHT1 conformer (which is related to the HH1 conformer by having a syn conformation of the 3′-G residue having the base flipped with respect to the 5′-G residue), we use the chemical shifts observed for (S,R,R,S-Bip)Pt(d(GpG)) (7.91 and 7.77 ppm for 3′-G and 5′-G, respectively). 59 This leads to estimated high temp- 60 Moreover, the chemical shifts are expected to be very little affected by the composition of the solvent in the case of a water and methanol mixture. Therefore, we can be confident that the high temperature spectrum reflects the coalescence set of signals of two dominating conformers, HH1 and ΔHT1 (and possibly some minor conformers).…”