³¹P NMR investigation of the backbone conformation and dynamics of the hexamer duplex d(5′-GCATGC)₂ in its complex with the antibiotic nogalamycin

Heteronuclear chemical shift correlation experiments confirm that the two down-field shifted ³¹P resonances in the spectrum of the (nogalamycin)₂-d(GCATGC)₂ complex correspond to the phosphodiesters CpA and TpG at the intercalation sites. ³¹P relaxation measurements (R₁, R₂ and {¹H}-³¹P NOE) at 4.7 and 9.4 T permit the correlation time of each phosphate to be determined together with their chemical shift anisotropies. Significant differences in deoxyribose H3′-³¹P coupling constants and chemical shift anisotropy contributions are observed, consistent with an asymmetric DNA backbone conformation for the phosphate groups at the intercalation sites. Large amplitude internal motions of the phosphates do not appear to contribute significantly to relaxation.