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^,

Abstract

Proteins that discriminate between cisplatin-DNA adducts and oxaliplatin-DNA adducts are thought to be responsible for the differences in tumor range, toxicity, and mutagenicity of these two important chemotherapeutic agents. However, the structural basis for differential protein recognition of these adducts has not been determined and could be important for the design of more effective platinum anticancer agents. We have determined high-resolution NMR structures for cisplatin-GG and undamaged DNA dodecamers in the AGGC sequence context and have compared these structures with the oxaliplatin-GG structure in the same sequence context determined previously in our laboratory. This structural study allows the first direct comparison of cisplatin-GG DNA and oxaliplatin-GG DNA solution structures referenced to undamaged DNA in the same sequence context. Non-hydrogen atom rmsds of 0.81 and 1.21 were determined for the 15 lowest-energy structures for cisplatin-GG DNA and undamaged DNA, respectively, indicating good structural convergence. The theoretical NOESY spectra obtained by back-calculation from the final average structures showed excellent agreement with the experimental data, indicating that the final structures are consistent with the NMR data. Several significant conformational differences were observed between the cisplatin-GG adduct and the oxaliplatin-GG adduct, including buckle at the 5′ G6•C19 base pair, opening at the 3′ G7•C18 base pair, twist at the A5G6•T20C19 base pair step, slide, twist, and roll at the G6G7•C19C18 base pair step, slide at the G7C8•C18G17 base pair step, G6G7 dihedral angle, and overall bend angle. We hypothesize that these conformational differences may be related to the ability of various DNA repair proteins, DNA binding proteins, and DNA polymerases to discriminate between cisplatin-GG and oxaliplatin-GG adducts. † This work was supported by NIH Grant CA8440 (to S.G.C.) and NIEHS Grant P30ES10126 (to J.A.S.). ‡ Coordinates are available from the Protein Data Bank (PDB): 2NPW for the averaged structure of the CP-GG adduct and 2NQ0 for the family of the 15 best structures, 2NQ1 for the averaged structure of undamaged DNA in the AGGC sequence context, and 2NQ4 for the family of the 15 best structures.

Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts

“…Our structures of the CP-and OX-GG adducts in the AGGC sequence context (17,18) were the first of Pt-GG adducts with a purine on the 5′ side of the adduct, and we did not observe a large positive slide and shift at the A5-G6 base-pair step of those adducts. Furthermore, for the T5-G6 base-pair step of the OX-TGGT adduct we observed a large positive slide, but a slightly negative shift.…”

“…Previous studies in our laboratory (17,18) (manuscript in preparation) and other laboratories (17)(18)(19)(20) have shown that imino proton resonance of the 5′G of a Pt-GG adduct is more solvent accessible than that of the 3′G. This data suggests that the DNA may be more distorted and/or flexible on the 5′ side of the adduct.…”

“…We have obtained high-resolution solution NMR structures of the OX-GG adduct (17), the CP-GG adduct and undamaged DNA (18) in the AGGC sequence context and the OX-GG adduct and undamaged DNA duplex (manuscript in preparation) in the TGGT sequence context. These were the first NMR solution structures of the OX-GG adduct and the first structures of any Pt-GG adduct in a DNA sequence context with a purine on the 5′ side of the adduct.…”

Comprehensive Comparative Analysis of the Morphological Changes in a 12-mer DNA Oligonucleotide upon Platination by Cisplatin, Oxaliplatin and BNP3029 (a Substituted Cyano ligand-based Platinum analogue) using Molecular Dynamics Simulation Studies

“…The following contacts observed in the NMR study are not seen in the x-ray structure of oxaliplatin-DNA: (i) hydrogen-bond contacts between 5'-NH 2 hydrogen of DACH with g6 phosphate backbone oxygen atom (H---O: 1.879 Å); and (ii) contacts between 3'-NH 2 and O4 atom of T8 (H---O: 2.849 Å) [18].…”

“…Platinum-DNA oligonucleotide adducts have been studied using crystallography [14][15][16], NMR [17,18], and computational approaches [19][20][21]. Crystallographic studies have previously been carried out on 12-mer DNA oligonucleotide adducts of cisplatin, oxaliplatin and JM118 (JM118 is the active metabolite of Satraplatin) by Lippard and coworkers [14][15][16].…”