Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry

Abstract

Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding.

Evaluation of flavonoids binding to DNA duplexes by electrospray ionization mass spectrometry

“…Higher values of fraction of bound DNA indicate greater DNAbinding affinities. It has also been demonstrated in several studies that the relative binding affinities measured by ESI-MS were in fairly good agreement with the results obtained using solution-phase techniques [41][42][43]. Here, the relative binding affinities of the flavonoids toward duplex 1 are shown in Figure 2 as an example.…”

“…An example of this characteristic fragmentation pattern is shown in Figure 3a for the 1:1 complexes containing duplex 1 and quercetin. This fragmentation pattern is the same as that obtained for the well-known anthrapyrazole intercalators [43], suggesting that these flavonoid aglycones are likely to bind to the DNA duplexes via intercalation. Moreover, the low abundances of product ions resulted from base loss are indicative of weaker DNA-binding affinities of the flavonoid aglycones than those conventional intercalators previously studied [5,29,39].…”

“…With an assumption that the ESI response factors of the free DNA and the drug/DNA complexes are identical, the relative intensities of the free and bound DNA in the mass spectra are expected to be proportional to their relative abundances in solution [34]. Therefore, the values of fraction of bound DNA can be used as a unique parameter to compare the relative binding affinities of drugs with DNA structures [41][42][43]. Higher values of fraction of bound DNA indicate greater DNAbinding affinities.…”

A study of the non-covalent interaction between flavonoids and DNA triplexes by electrospray ionization mass spectrometry

“…Electrospray ionization mass spectrometry (ESI-MS) has proved to be a powerful tool for drug discovery and examining drug/DNA complexes with advantages such as determination of precise stoichiometry, low sample consumption and short analysis time [24,25]. Many drug/DNA complexes have been extensively studied by ESI-MS, and the results have agreed well with those obtained using solution phase techniques [26][27][28][29][30][31][32][33][34][35][36][37]. The flavonoid/duplex DNA complexes were first investigated using ESI-MS in our laboratory [26].…”

“…When the concentration of analyte is increased, nonspecific complexes may be detected in ESI mass spectra [29,37,46]. The concentration effects were investigated with mixtures where the DNA concentration was fixed at 10 M and the flavonoid concentrations were varied (5, 10, 20, 40 or 80 M).…”