Positive ion electrospray ionization mass spectrometry of double‐stranded DNA/drug complexes

Abstract

Positive ion electrospray ionization mass spectra of 16 base-pair double-stranded (ds)DNA have been obtained with essentially no ions from single-stranded DNA present. Single-stranded DNA was minimized by: (1) careful choice of DNA sequences; (2) the use of a relatively high salt concentration (0.1 M ammonium acetate, pH 8.5), and, (3) a low desolvation temperature (40 degrees C). Similarly, ESI-MS complexes of dsDNA with cisplatin, daunomycin and distamycin were obtained that contained only negligible amounts of single-stranded DNA. The complexes with daunomycin and distamycin were more stable to strand separation in the gas phase than dsDNA alone. This is in agreement with solution studies and with other recent gas phase results. These data contrast with many earlier ESI-MS studies of dsDNA and DNA/drug complexes in which ions from ssDNA are also normally observed.

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

“…In order to ensure that equimolar amounts of complementary strands were used in each experiment, single complementary strands were titrated against one another as previously described [14]. The relative amounts of the strands required to form 1:1 dsDNA calculated from these titrations were then used in all experiments.…”

“…Mixtures of dsDNA with [Ru(phen) 2 dpq]Cl 2 or [Ru(phen) 2 dpqC]Cl 2 were prepared as previously described [15]. It should be noted that in our laboratory we have established that no significant differences in the relative abundances of drug-dsDNA complexes are observed when the drugs are added either after or during annealing of the DNA with the non self-complementary 16 mers used in these experiments [6,14].…”

“…There have been several recent reports of ESI mass spectra of DNA acquired using positive ion mode [14, 16 -20]. Our own work has shown that negative and positive ion ESI mass spectra of Dm/ dsDNA mixtures obtained under otherwise identical experimental conditions were substantially different [14]. In negative ion spectra, the most abundant ions were from the dsDNA ϩ 2 Dm complex, whereas in positive ion mode, the most abundant ions were from the dsDNA ϩ 1 Dm complex.…”

“…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].…”

A eole for the MS analysis of nucleic acids in the post-genomics age

“…Direct ESI-MS analysis of nucleic acid complexes with other nucleic acids [106 -110], proteins [111][112][113][114][115][116], and small molecule ligands [117][118][119][120] can reveal their exact composition and stoichiometry from the observed molecular mass, dispensing with the typical curvefitting of bulk data required by spectroscopic and calorimetric methods. Unlike these techniques, MS is capable of resolving any free/bound species at equilibrium in solution, even when such species possess very similar spectroscopic characteristics.…”