Evaluation of alkaloids binding to the parallel quadruplex structure [d(TGGGGT)]4 by electrospray ionization mass spectrometry

In this study, electrospray ionization mass spectrometry (ESI‐MS) was used to investigate the binding interaction of six alkaloids with parallel intermolecular G‐quadruplex d(TGGGGT)]₄, and five alkaloids including berberine, jatrorrhizine, palmatine, tetrandrine, and fangchinoline showed complexation with the target DNA. Relative binding affinities were estimated on the basis of mass spectrometric data. The slight differences in chemical structures of berberine, jatrorrhizine, and palmatine had little influence on their binding affinities to d(TGGGGT)]₄. Tetrandrine and fangchinoline selectively bound to d(TGGGGT)]₄ versus duplex DNA. Collision‐induced dissociation (CID) experiments showed that the complexes with berberine, jatrorrhizine, and palmatine dissociated via strand separation and ligand retaining in the strand while the complexes with tetrandrine and fangchinoline were dissociated via ligand elimination. A comparison of dissociation patterns in CID experiments of complexes with the alkaloids to those with the traditional G‐quadruplex DNA binders suggested an end‐stacking binding mode for tetrandrine and fangchinoline and an intercalation binding mode for berberine, jatrorrhizine, and palmatine to the target DNA. The current work not only provides deep insight into alkaloid/d(TGGGGT)]₄ complexes and useful guidelines for design of efficient anticancer agents but also demonstrates the utility of ESI‐MS as a powerful tool for evaluating interaction between ligand and quadruplex DNA. Copyright © 2012 John Wiley & Sons, Ltd.