Relationship of Solution and Protein-Bound Structures of DNA Duplexes with the Major Intrastrand Cross-Link Lesions Formed on Cisplatin Binding to DNA

Abstract

DNA bases in the three-base-pair (3bp) region of duplexes with the two major lesions of cisplatin (cis-PtCl(2)(NH(3))(2)) with DNA, namely d(XGG) and d(XAG) ( = N7-platinated base), differ in their relative positions by as much as approximately 3.5 A in structures in the literature. Such large differences impede drug design and assessments of the effects of protein binding on DNA structure. One recent and several past structures based on NMR-restrained molecular dynamics (RMD) differ significantly from the reported X-ray structure of an HMG-bound XGG 16-mer DNA duplex (Ohndorf, U.-M.; Rould, M. A.; He, Q.; Pabo, C. O.; Lippard, S. J. Nature 1999, 399, 708). This 16-mer structure has several significant novel and unique features (e.g., a bp step with large positive shift and slide). Hypothesizing that novel structural features in the XGG or XAG region of duplexes elude discovery by NMR methods (especially because of the flexible nature of the 3bp region), we studied an oligomer with only G.C bp's in the XGGY site by NMR methods for the first time. This 9-mer gave a 5'-G N1H signal with a normal shift and intensity and showed clear NOE cross-peaks to C NHb and NHe. We assigned for the first time (13)C NMR signals of a duplex with a GG lesion. These data, by adding NMR-based criteria to those inherent in NOESY and COSY data, have more specifically defined the structural features that should be present in an acceptable model. In particular, our data indicated that the sugar of the X residue has an N pucker and that the GG cross-link should have a structure similar to the original X-ray structure of cis-Pt(NH(3))(2)(d(pGpG)) (Sherman S. E.; Gibson, D.; Wang, A. H.-J.; Lippard, S. J. J. Am. Chem. Soc. 1988, 110, 7368). With these restrictions added to NOE restraints, an acceptable model was obtained only when we started our modeling with the 16-mer structural features. The new X-ray/NMR-based model accounted for the NOESY data better than NOE-based models, was very similar in structure to the 16-mer, and differed from solely NOE-based models. We conclude that all XGG and XAG (X = C or T) duplexes undoubtedly have structures similar to those of the 16-mer and our model. Thus, protein binding does not change greatly the structure of the 3bp region. The structure of this region can now be used in understanding structure-activity relationships needed in the design of new carrier ligands for improving Pt anticancer drug activity.

Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder; an NMR and molecular dynamics study

“…Furthermore, it has been suggested that the H2' signal should be rather sensitive to deviations from regular double helical conformation [44][45][46]. For example, a large upfield shift of H2' in a cis-platinated duplex was attributed to shielding by the destacked adenine base of the kinked structure [46].…”

“…Furthermore, it has been suggested that the H2' signal should be rather sensitive to deviations from regular double helical conformation [44][45][46]. For example, a large upfield shift of H2' in a cis-platinated duplex was attributed to shielding by the destacked adenine base of the kinked structure [46]. It is now well established that Y-R steps (Y= pyrimidine, R= purine) like CpG are geometrically flexible [47] and several studies have shown that CpG steps are involved in DNA bending [48,49].…”

Solution Structures of a DNA Dodecamer Duplex with and without a Cisplatin 1,2-d(GG) Intrastrand Cross-Link: Comparison with the Same DNA Duplex Containing an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link,

“…Previous NMR studies of Pt-GG adducts have examined a single type of adduct (CP or OX) in a single sequence context and have compared both the proton chemical shifts and NOE cross-peak intensities with average values for undamaged B-DNA in a variety of sequence contexts (24,25,27,33) (34). However, it is unclear whether some of the observed differences are due to differences in sequence context rather than between the platinated and unplatinated strand.…”

“…However, downfield chemical shifts have been reported for the H8 protons of the 5′ and 3′ G residues for all Pt-GG adducts studied to date (24)(25)(26)33), so this has been considered a universal feature of Pt-GG adducts. In their analysis of a CP-GG adduct, Marzilli et al (25) reported a much greater downfield chemical shift for the H8 proton on the 5′ G residue than for the 3′ G residue and a significant upfield shift of the H2′ proton on the C complementary to the 5′ G residue, which they considered universal features of all CP-GG adducts. However, we do not observe either of these features in direct comparisons of the CP-GG DNA (Table S1) adducts with undamaged DNA (Table S2), so these chemical shifts do not appear to be features of all CP-GG adducts.…”

“…We also see some significant difference in NOE cross-peak intensities between CP-GG and OX-GG adducts. Marzilli et al (25) had previously suggested that an unusually weak NOE cross-peak between H2′ of the C complementary to the 5′ G residue and H6/H8 of the base complementary to the 5′ flanking base was a universal feature of all CP-GG adducts. Here, we find that the C19 H2′-T20 H6 NOE cross-peak for the CP-GG adduct in the AGGC sequence context is also weaker than that in undamaged DNA (Table S3).…”