NMR solution structure of a DNA decamer containing an interstrand cross-link of the antitumor drug cis-diamminedichloroplatinum (II).

ABSTRACT

A 10 base pairs double-stranded oligonucleotide with the sequence d(CCTCG.CTCTC). d(GAGAG.CGAGG) containing a single interstrand cross-link resulting from chelation of the N7 position of two guanine residues on the opposite strands of DNA at the d(G.C/G.C) site by a cis-diammineplatinum(II) residue was analyzed by 1H NMR spectroscopy. All the exchangeable and nonexchangeable protons resonance lines (except some H5'-H5") were assigned. NOESY spectra and chemical shifts indicated that the cross-linkage of the guanines of G.5 and G.6 induced extrahelicity of C5 and C6. Moreover, several unusual proximities were observed such as (i) NOE cross-peaks between the H2'-H2" of G.5 or G.6 and the aromatic proton of their 5' neighbor C4 or A7 (ii) the absence of cross-peak for the steps G.5-C6, C6-T7 and C5-G4 (iii) a strong NOESY connectivity between H8(G.5) and H2(A7). All these data allowed us to describe the head to tail arrangement of the two cross-linked guanines as well as their stacking with flanking neighbor nucleotides (G.5 with T7.A7 base pair and G.6 with C4.G4 base pair). Using all the NOESY and TOCSY data (208 constraints), we have obtained a solution structure of the cross-linked duplex by using the NMR-constrained molecular mechanics program JUMNA. The reversal position of the two cross-linked guanines placed the cis-diammineplatinum(II) residue in the minor groove. The stacking of the two cross-linked guanines with the surrounding bases induced a bend of 40 degrees toward the minor groove. The locally left-helix formation, the extrusion of the cytosines and the stacking of the platinated guanines led to an unwinding of 76 degrees. This value is in good agreement with the values deduced from gel electrophoresis experiments.