Interaction between antitumor drugs and a double-stranded oligonucleotide studied by electrospray ionization mass spectrometry

Abstract

Electrospray ionization mass spectrometry has been used to investigate the complex formation between a double-stranded oligonucleotide and various antitumor drugs belonging to two categories: intercalators (ethidium bromide, amsacrine and ascididemin) and minor groove binders (Hoechst 33258, netropsin, distamycin A, berenil and DAPI). The goal of this study is to determine whether the relative intensities in the mass spectra reflect the relative abundances of the species in the solution phase. The full scan MS spectra suggest non-specific binding for the intercalators and specific binding for the minor groove binders. The preferential stoichiometries adopted by each minor groove binder have been determined by studying the influence of the drug concentration on the spectra. We obtained 2:1 > 1:1 for distamycin, 1:1 > 2:1 for Hoechst 33258 and DAPI, and only the 1:1 complex for netropsin and berenil. These features reflect their known behavior in solution. The compared MS/MS spectra of the 1:1 complexes with Hoechst and netropsin, when correlated to published crystallographic data, suggest the possibility to infer some structural information. The relative binding affinities of the drug for the considered duplex have been deduced with two by two competition experiments, assuming that the relative intensities reflect the composition of the solution phase. The obtained affinity scale is the following: netropsin > distamycin A > DAPI > Hoechst 33258 > berenil. These examples show some of the potential uses of mass spectrometry as a useful tool for the characterization of specific drug binding to DNA, and possibly a rapid drug screening method requiring low amounts of materials.

Evaluation of complexes of DNA duplexes and novel benzoxazoles or benzimidazoles by electrospray ionization mass spectrometry

“…In the study by Gabelica, the DNA-binding modes observed in the gas-phase for ethidium bromide, amsacrine, and ascididemin exhibited the non-specific multiple-drug binding which parallels the binding behaviors observed in solution [16]. However, the relative peak intensities also paralleled ligand polarity, including ligand charge, and thus the observed binding pattern could simply be an artifact of the electrospray process.…”

“…The lack of a well-defined DNA binding stoichiometry by the antibiotic analogs is reminiscent of results reported by Gabelica et al for drug-DNA complexes containing known intercalators such as ethidium bromide, amsacrine, and ascididemin [16]; as well as Kapur et al for the more complex intercalators daunomycin and nogalamycin [36]. In the study by Gabelica, the DNA-binding modes observed in the gas-phase for ethidium bromide, amsacrine, and ascididemin exhibited the non-specific multiple-drug binding which parallels the binding behaviors observed in solution [16].…”

“…Likewise, the ion at m/z 1008 could be [ss Ϫ 3H] Ϫ3 or [ds Ϫ 6H] Ϫ6 , although expansion of this ion and examination of the sodium adduct satellite peaks suggests that the identity is [ss Ϫ 3H] Ϫ3 . Although apparent duplex ions could result from non-specific aggregation of single strands during the electrospray process, this has previously been shown to be minimized or eliminated under similar solvent conditions and ODN concentrations as was used in this study [16,17]. Thus, for the studies presented here, the duplex DNA peaks observed in the electrospray mass spectra are assumed to result from specific association of the self-complementary strands.…”

“…The use of self-complementary ODNs produces readily interpretable mass spectra with peaks generally composed of single ion species [16,17]. The unambiguous assignment of even charge state duplex ions cannot be made due to overlap of the m/z ratios for duplex ions and single-stranded ions of half the charge.…”

Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry

“…For example, distamycin binds in a 1:1 complex along AT-rich minor grooves of double-stranded (ds) DNA, but NMR studies suggest that it also binds in a head-to-tail fashion in a 2:1 complex with DNA [13]. Both of these stoichiometries have been observed in ESI-MS experiments [10,11,14].…”