Proton nuclear magnetic resonance study of the self-complementary hexanucleotide d(pTpA)3 and its interaction with daunomycin

Abstract

The helix-coil transition of the self-complementary hexanucleotide d(pTpA)3 was studied in 1 M NaCl by high-resolution proton NMR spectroscopy. Almost all of the 12 resonances deriving from the 3 environments of the 4 nucleotide protons were assigned to the central, internal or terminal nucleotides. At 5.degree. C, the effect of extensive fraying is evident since the central base pairs exhibit only 20% of the chemical shifts observed for poly(dA-dT).cntdot.poly(dA-dT) accompanying denaturation. Daunomycin interacts with the hexanucleotide duplex at 5.degree. C and stabilizes it by 21.degree. C at a drug/nucleotide ratio of 0.063 (i.e., drug/hexanucleotide duplex ratio of 0.75). The chemical shifts of the drug protons suggest that ring D of daunomycin does not overlap significantly with the central base pairs of the hexanucleotide and that it extends out from the helix. This information, together with studies of space-filling models of the complex, suggests that rings B and C of daunomycin overlap with adjacent base pairs and are skewed with respect to the base pairs. [Daunomycin and its analog, adriamycin, are used extensively for the treatment of a variety of forms of cancer.].