Spectrometric studies of cytotoxic protoberberine alkaloids binding to double-stranded DNA

The noncovalent complexes of five cytotoxic protoberberine alkaloids, that is, berberine, palmatine, jatrorrhizine, coptisine, and berberrubine with several double-stranded oligodeoxynucleotides were systematically investigated by using electrospray ionization mass (ESI-MS) and fluorescence spectrometric methods, with the aim of establishing the structure-activity relationships. ESI-MS spectrometric studies indicated that these five alkaloids showed both 1:1 and 1:2 binding stoichiometries with d(AAGAATTCTT)(2), d(AAGGATCCTT)(2), and d(AAGCATGCTT)(2). Their relative binding affinities toward these three double-stranded DNA were semi-quantitatively evaluated by measuring the ratios of the complex signals ([ds+alkaloid-5H](4-)+[ds+2alkaloid-6H](4-)) to those of the duplexes ([ds-4H](4-)) and also by ESI-MS competitive binding experiments. These experiments established the relative binding affinities of five protoberberine alkaloids in the order of palmatine>jatrorrhizine>coptisine>berberine>berberrubine with d(AAGAATTCTT)(2), palmatinecoptisine>jatrorrhizineberberine>berberrubine with d(AAGGATCCTT)(2) and palmatine>jatrorrhizinecoptisine>berberine>berberrubine with d(AAGCATGCTT)(2). Significantly, these alkaloids except berberrubine bound to d(AAGGATCCTT)(2) and d(AAGCATGCTT)(2) with the affinities comparable to Hoechst 33258, a typical DNA minor groove binder. The relative binding preferences of berberine, palmatine, and coptisine with these three double-stranded DNA were further quantitatively assessed by their association constants obtained from fluorescence titration experiments. The values revealed the order of relative binding affinities as berberine>coptisine>palmatine with d(AAGAATTCTT)(2) and coptisine>berberine>palmatine with d(AAGGATCCTT)(2) and d(AAGCATGCTT)(2). These results were not in full agreement with those obtained from ESI-MS experiments, maybe due to the different measuring solution conditions. The results from ESI-MS and fluorescence titration experiments indicated that the sequence selectivities of these five alkaloids were not significant and remarkable AT- or GC-rich DNA binding preferences were not obtained, in contrast to the report that berberine binds preferentially to AT-rich DNA. To provide further insight into the sequence selectivities, the association constants of berberine with d(AAGATATCTT)(2), 5'-AAGTAATCTT-3'/5'-AAGATTACTT-3', d(AAGGGCCCTT)(2), d(AAGGCGCCTT)(2), and 5'-AAGGCCGCTT-3'/5'-AAGCGGCCTT-3', that is double helical DNA from AT-rich to GC-rich sequences, were further measured by fluorescence titration methods. No significant differences in their association constants were observed, suggesting that berberine showed no remarkable sequence selectivities.