NMR solution structure of a DNA 12/11-mer:: d(CTCCTGTGTCTC)•d(GAGATA-AGGAG) containing a transplatin interstrand G-N7/A-N1 cross-link

The solution structure of a double-stranded DNA. oligonucleotide, d(CTCCTG*TGTCTC).d(GAGATA*-AGGAG), containing a trans-diammineplatinum(II) interstrand cross-link (the asterisks indicate the two cross-linked bases) has been determined by means of two-dimensional nuclear magnetic resonance (2D NMR) and NOE-restrained molecular dynamics and energy minimization refinement. The crosslinked duplex was prepared in two steps. First, trans-diamminedichloroplatinum(II) was reacted with the single-stranded d(CTCCTGTGTCTC), which resulted in the formation of a stable (G1,G3)-intrastrand cross-link. Then, the platinated oligonucleotide was hybridized with the partially complementary oligonucleotide d(GAGATA-AGGAG), in which the d(AT) doublet facing the intrastrand GTG cross-link replaced the d(CAC) triplet in a regular duplex. The formation of the hybrid promoted the rearrangement of the (G1,G3)-intrastrand cross-link into an interstrand cross-link. The NMR experiments were performed in 0.5 m NaCl solution. All the exchangeable and nonexchangeable proton resonances (except some H5'/H5 " signals) of the major species could be assigned. NOESY spectra and chemical shift data indicate that the interstrand cross-link is established between G6-N7 and A18-N1. The platinated G residue is rotated about the glycosyl bond from an anti conformation into a syn conformation. The two imino protons G8-H1 and T17-H3 forming hydrogen bonds in the mismatched base pair, G8-T17, give rise to signals (upfield as expected) at delta = 10.52 and delta = 10.82. Using all the NOESY data (215 constraints) from a 0.8 mm sample, a solution structure of the cross-linked duplex has been obtained by NOE-restrained molecular dynamics/mechanics refinements. Only the central portion of the duplex deviates significantly from regular B-form geometry. The base residue T7 in the context GTG in the top strand is located in an extrahelical position. The interstrand cross-link induces a bend of 21 degrees in the duplex.