Interactions of antitumor drugs with natural DNA: proton NMR study of binding mode and kinetics

Abstract

1H NMR has been used to study the interactions of over 70 clinical and experimental antitumor drugs with DNA. Spectra of the low-field (H-bonded imino proton) resonances of DNA were studied as a function of drug per base pair ratio. From the spectral changes observed, it was possible to distinguish three modes of drug binding (intercalation, groove binding, and nonspecific outside binding), to determine the kinetics of drug binding (approximate lifetime of the bound drug), and, in favorable cases, to determine the specificity of the drugs for A X T or G X C base pairs. This method is a useful assay for general drug-binding characteristics. For the intercalating compounds there appears to be a correlation between drug-binding kinetics and useful antitumor activity.

Distamycin-induced inhibition of homeodomain-DNA complexes.

“…This is in contrast to the long lifetimes of 80-100 min in the presence of 50 nM (in duplex) unlabelled BS2-18 wt DNA which agrees well with the value of 90 min determined previously (Affolter et al, 1990a). Based on the results of these measurements and: (i) the experimentally determined lifetimes of distamycin of -0.1-2 s in various AT-containing binding sites (Feigon et al, 1984;Pelton andWemmer, 1989, 1990); and (ii) the ability of distamycin to induce conformational changes of the DNA upon binding, we propose the following mechanism. Distamycin binds in the minor groove of the DNA adjacent to Antp HD thus forming a ternary complex and simultaneously changing the local conformation of the DNA.…”

“…In addition, it has already been shown for several systems that the biological activity of a DNA ligand correlates better with the kinetics of its binding rather than with its affinity constant to DNA (e.g. Mdller and Crothers, 1968;Feigon et al, 1984;Skorobogaty et al, 1988).…”

Complexation of norfloxacin with DNA in the presence of caffeine

“…NOR binds more tightly to the double-stranded form of the oligonucleotide in solution. Even so the complexation parameters for this reaction (K 12 and enthalpy/entropy) are much smaller in absolute value compared with the three-ring intercalators [12,21] but much larger than that calculated above for self-association of NOR and its hetero-association with CAF (Tables 1,2 Tables 1,3), which is known to be a distinctive feature of intercalation [21,23,24], supports this conclusion. Secondly, the decrease in magnitude of the complexation parameters is apparently due to a smaller contribution from π-π stacking arising when the two fused-ring NOR chromophore is intercalated between the adjacent bases along the oligomer sequence.…”

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

“…These observations suggest a different mode of interaction of Tpy with the double strand when located at the 3' or 5' end, correlating with differences in the stabilization abilities of these conjugates. Although the upfield shifts of imino protons following conjugation of Tpy suggest an intercalative mode of binding [23], we never noticed clear stabilizing properties of free Tpy ligands for double stranded DNA [12]. A partial dynamic intercalation of the unmetalated Tpy could account for the observed dynamic of 3' base pairs.…”