TY - JOUR
T1 - Spectrometric studies of cytotoxic protoberberine alkaloids binding to double-stranded DNA
AU - Chen, Wen Hua
AU - Qin, Yong
AU - CAI, Zongwei
AU - Chan, Chi Leung
AU - Luo, Guo An
AU - JIANG, Zhi Hong
N1 - Funding Information:
The authors are grateful to Professor Irving H. Goldberg, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, for his critical reading of the manuscript. We are grateful to Professor Shou-Xun Zhao of China Pharmaceutical University for providing some protoberberine alkaloids. This work was financially supported by the Faculty Research Grants from Hong Kong Baptist University and Research Grants Council, University Grants Committee of Hong Kong.
PY - 2005/3/1
Y1 - 2005/3/1
N2 - 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, palmatine ≥ coptisine > jatrorrhizine ≥ berberine > berberrubine with d(AAGGATCCTT)2 and palmatine > jatrorrhizine ≥ coptisine > 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.
AB - 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, palmatine ≥ coptisine > jatrorrhizine ≥ berberine > berberrubine with d(AAGGATCCTT)2 and palmatine > jatrorrhizine ≥ coptisine > 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.
KW - DNA
KW - Noncovalent interaction
KW - Protoberberine alkaloids
KW - Spectrometry
UR - http://www.scopus.com/inward/record.url?scp=13444292203&partnerID=8YFLogxK
U2 - 10.1016/j.bmc.2004.10.049
DO - 10.1016/j.bmc.2004.10.049
M3 - Journal article
C2 - 15698803
AN - SCOPUS:13444292203
SN - 0968-0896
VL - 13
SP - 1859
EP - 1866
JO - Bioorganic and Medicinal Chemistry
JF - Bioorganic and Medicinal Chemistry
IS - 5
ER -