FACTORS AFFECTING DNA-SEQUENCE SELECTIVITY OF NOGALAMYCIN INTERCALATION - THE CRYSTAL-STRUCTURE OF D(TGTACA)(2)-NOGALAMYCIN(2)

As part of an investigation into the sequence selectivity of the nogal amycin-DNA interaction, the 1.58 Angstrom structure of nogalamycin com plexed with d(5')(TGTACA)(2) has been determined by single-crystal X-r ay analysis. The complex crystallised in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions a = 26.3 Angstrom, b = 52.0 Angstro m and c = 67.1 Angstrom, incorporating two B-DNA duplexes and four nog alamycin molecules in the asymmetric unit. The final refined structure included 97 water molecules, one spermine molecule, two acetate ions and one sodium ion, yielding an overall R factor of 19.2% (calculated using all 12,358 reflections in the resolution range 10.7 to 1.6 Angst rom) and an R(free) of 23.7% (using 1229 test reflections). The d(5')( TGTACA)(2) sequence was designed to include the d(5')(TpG) pyrimidine- purine base step that has been ascertained as a preferential intercala tion site. The complexes in the asymmetric unit are globally similar; one nogalamycin molecule intercalates between each d(5')(TpG) step in each duplex. The DNA of each complex exists as a distorted B-DNA duple x displaying some Z-DNA character in the form of C3' endo sugars at so me residues. Structural comparisons between the d(5')(TGTACA)(2)-nogal amycin(2) complex and the complexes of this drug with the sequences d( 5')(TGATCA)(2) and d(5')((5Me)CGT(pS)A(5Me)CG)(2) highlight difference s in binding interactions between nogalamycin and these various triple t DNA binding sites, with regards to the stability of drug intercalati on, which in turn is correlated to effective levels of cytotoxicity to wards tumour cells. The number of both direct and water-mediated hydro gen bonds and van der Waal's interactions between substituents of noga lamycin and the d(5')(TGTACA)(2) and d(5')((5Me)CGT(pS)A(5Me)CG)(2) se quences are significantly greater than those made with the d(5')(TGATC A)(2) sequence, suggesting that the central d(5')(TpA) in the former c onfers additional stability to the complex once the drug has bound. (C ) 1996 Academic Press Limited