The critical DNA lesion accounting for the anticancer activity of cis-PtCl2(NH3)2 and its analogues [cis-PtX2A2:  A2 = a diamine or two amines, X2 = anionic leaving ligand(s)] is an unusual intrastrand cis-Pt(d(GpG))A2 cross-link with Pt linking N7's of adjacent guanines (G). The only known cross-link form with two anti G's, HH1, has head-to-head (HH) bases. We provide NMR, HPLC, and mass spectral evidence for a second, distinct HH cis-Pt(d(GpG))A2 cross-link conformer, HH2, in BipPt(d(GpG)) (Bip = 2,2‘-bipiperidine, where the coordinated Bip has R, S, S, and R configurations at the asymmetric N, C, C, and N chelate ring atoms). The HH1 and HH2 BipPt(d(GpG)) conformers are formed both kinetically and thermodynamically in comparable amounts. The NMR results showed for both BipPt(d(GpG)) conformers that the bases were anti, anti HH, the 5‘-G sugar pucker was N, and the 3‘-G sugar pucker was S. The major difference between the HH1 and HH2 conformers is the propagation direction of the phosphodiester linkage. Molecular modeling calculations with NMR restraints on the HH1 and HH2 conformers indicate comparable energies and no unusual features that should have precluded prediction of the existence of the HH2 conformer. Calculations led to similar conclusions for the cis-Pt(d(GpG))(NH3)2 HH2 conformer. During the two decades of intense interest in this cross-link, this new form has gone unrecognized, although published results have suggested the presence of unknown conformers. Our results in this first report of a second anti, anti HH d(GpG) adduct place an entirely different perspective on the conformational diversity of cis-Pt(d(GpG))(NH3)2 in solution. Although the new HH2 conformation is unlikely to exist in a duplex at low temperature, the new form may be important in mutational events, in duplex breathing, or in duplex interactions with DNA damage recognition proteins and repair enzymes. Finally, the spectral features, especially the H8 NMR signals, of HH1 d(GpG) species in single strands and in duplexes are typically very different, results attributed to differences in both extent and direction of base canting. Bip is an example of a chirality controlling chelate (CCC) ligand that can influence canting. The HH1 conformer of BipPt(d(GpG)) is the first single-stranded species that has key spectral characteristics very similar to those of a typical duplex cross-linked species. Thus, even the HH1 conformer of BipPt(d(GpG)) is an unusual species.

N7−Pt−N7 d(GpG) intrastrand cross-link adducts are formed in DNA by the anticancer drug, cisplatin. By creating adducts with slow dynamic motion, we have identified a new abundant conformer with the guanine bases in a head-to-tail (HT) arrangement and with both sugars in the N pucker of A-form DNA instead of the S pucker of B-form DNA. Both features are unprecedented for such cross-links. The HT form is one of two abundant thermodynamic and kinetic products formed by addition of d(GpG) to [(S,R,R,S)-BipPt(H2O)2]2+ (Bip = 2,2‘-bipiperidine with S, R, R, and S configurations at the asymmetric N, C, C, and N chelate ring atoms). The second form has the common head-to-head conformation (HH1) with the backbone propagating in the normal direction, both G's anti and with N and S puckers for the 5‘- and 3‘-G residues, respectively. This form has a typical NMR shift pattern:  upfield 5‘-G H8, downfield 3‘-G H8, and downfield 31P NMR signal. In contrast, the HT (S,R,R,S)-BipPt(d(GpG)) form has several unusual or unique NMR spectral features, including pronounced upfield shifts of both G H8 signals, unusually shifted 5‘-G H3‘ and 3‘-G H2‘ signals, and an unexpectedly upfield-shifted 31P NMR signal. A strong 3‘-G H8−H1‘ NOE cross-peak, the absence of an H8−H8 NOE cross-peak, and H1‘ couplings establish that this form is an HT conformer with a syn 3‘-G, an anti 5‘-G, and both sugars having mainly N pucker. The HT base orientation in cross-links introduces chirality, and two conformers, ΔHT1 and ΛHT2, are possible with normal and opposite directions of backbone propagation, respectively. NMR-restrained molecular mechanics and dynamics calculations show that the ΔHT1 conformer has the lower energy. Of some interest, rules in the literature cannot account for the G H8 shifts of any BipPt(d(GpG)) form reported by us here and previously. We advance new rules that allow successful G H8 shift predictions for these cross-links and also for cisplatin oligonucleotide adducts; these rules are consistent with the solid-state structure of cis-Pt(NH3)2(d(pGpG)) (Sherman, S. E.; Gibson, D.; Wang, A. H.-J.; Lippard, S. J. J. Am. Chem. Soc. 1988, 110, 7368−7381), but they conflict with widely held interpretations of cis-Pt(NH3)2(d(GpG)) solution structure and dynamics. Finally, our results suggest that, in the future, the effect of the carrier ligands on the HH vs HT cross-link conformation must be considered in drug design.

Chirality-controlling chelate (CCC) ligands are a class of chiral diamine ligands with one or two chiral secondary amine ligating groups. Analogues of platinum anticancer agents containing CCC ligands exhibit unusual steric and dynamic features. In this study NMR and CD methods were used to evaluate the influence of the N9 substituent in guanine derivatives (G) on conformer distribution in one class of (CCC)PtG(2)() complexes. We employed the CCC ligand, N,N'-dimethyl-2,3-diaminobutane [Me(2)()DAB with S,R,R,S or R,S,S,R configurations at the four asymmetric centers, N, C, C, and N]. For each Me(2)()DABPtG(2) complex, the presence of four G H8 signals demonstrated formation of all three possible atropisomers: DeltaHT (head-to-tail), LambdaHT, and HH (head-to-head). Different G ligands (5'-GMP, 3'-GMP, 1-MeGuo, Guo, or 9-EtG) were chosen to assess the effect of the N9 substituent on the relative stability and spectral properties of the atropisomers. The conformations of the atropisomers of Me(2)()DABPtG(2) were determined from CD spectra and from NOE cross-peaks (assigned via COSY spectra) between G H8 signals and those for the Me(2)()DAB protons. Regardless of the N9 substituent, the major form was HT. However, this form had the opposite chirality, LambdaHT and DeltaHT, and base tilt direction, left- and right-handed, respectively, for the S,R,R,S and R,S,S,R configurations of the Me(2)()DAB ligand. Thus, the chirality of the CCCligand, not hydrogen bonding, is the most important determinant of conformation. For each Me(2)()DABPtG(2) complex, the tilt direction of all three atropisomers is the same and, except for 5'-GMP, the order of abundance was major HT > minor HT > HH. For 5'-GMP, the HH atropisomer was three times as abundant as the minor HT species, suggesting that phosphate-NH(Me(2)()DAB) hydrogen bonds could be present since such bonding is possible only for the 5'-GMP derivatives. However, if such phosphate-NH hydrogen bonds exist, they are weak since the percentage of the major HT form of 5'-GMP complexes is similar and indeed can be smaller compared to this percentage for complexes with other G's. The CD spectra of all (S,R,R,S)-Me(2)()DABPtG(2) complexes were similar and opposite to those of all (R,S,S,R)-Me(2)()DABPtG(2) complexes, indicating the CD signature is characteristic of the dominant HT conformer, which has a chirality dictated by the chirality of the CCC ligand and not the N9 substituent.