Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex

Oxaliplatin (OX), a second-generation platinum drug recently approved by the FDA for the treatment of colorectal cancer, differs from cisplatin (CP) by addition of a cyclohexane ring to the amines of cisplatin to form a diaminocyclohexane (DACH) ring. Although it has been shown that OX has a similar adduct formation profile to that of cisplatin, one would anticipate the GG adduct to be structurally dissimilar once the drugs are bound to DNA. We have determined the three-dimensional solution structure of the DNA dodecamer d(CCTCAGGCCTCC)·d(GGAGGCCTGAGG) by 2D NMR. Of 249 protons, only ten protons of H5' and H5'' are unassigned due to resonance overlap, resulting in ~ 96% proton assignment. From the cross-peak volume of H1 and water and temperature dependence of H1, it can be concluded that the G6* H1 exchanges with water much more rapidly than the G7* H1. The estimated distance of G*6 H8-G*7 H8 from NOE cross-peaks is 3.2 Å (5 Å is normal for B-DNA), consistent with coordination of Pt to these residues in a head-to-head fashion. In the H1'-H6/H8 region, the A5 H1'-G*6 H8, G*6 H1'-G*7 H8 cross-peaks were weaker than the equivalent cross-peaks from the flanking B-DNA regions indicating distances larger than those in normal B-DNA. These NOE cross-peak patterns are consistent with those found in the previous reported NMR solution structure of a CP- 9mer DNA duplex (1). The structure of the duplex was calculated using the program CNS with a simulated annealing protocol. A total of 284 distance restraints were employed in the structure calculation. These restraints were derived from NOE cross peaks, of which 120, 133, 31 were intraresidue, interresidue and crossstrand NOEs, respectively. In addition, 60 distance restraints for hydrogen bonds were imposed on Watson?Crick base pairs; however, for base pairs associated with the OX adduct, only N1-N3 hydrogen bonds were retained.

Planarity was also restrained for all base pairs with the exception of the base pairs associated with the OX, where the force constant was reduced by half. No backbone dihedral angles were restrained. A high-resolution solution structure has been obtained The structure shows an overall axis bend of 30°, which is similar to the recently reported crystal structure of the OX adduct (2), but is very different from a recent NMR structure for the CP adduct (ibid). Comparisons between the conformation of CP and OX AGG adducts has been discussed in detail. (Supported by NIH grant CA84480).

Yibing Wu*
Padmanava Pradhan
Jody Havener
Sharon L. Campbell
Stephen G. Chaney

Department of Biochemistry and Biophysics
University of North Carolina
Chapel Hill, NC 27599
101 Manning Dr
Chapel Hill, NC 27599
Phone: 919-966-3286
Fax: 919-966-966-2852

References and Footnotes
  1. Marzilli et al, J. Am. Chem. Soc. 123, 2764-2770 (2001).
  2. Spingler et al, Inorg. Chem. 40, 5596-5602 (2001)