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

Wen Hua Chen*, Yong Qin, Zongwei CAI, Chi Leung Chan, Guo An Luo, Zhi Hong JIANG

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

73 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1859-1866
Number of pages8
JournalBioorganic and Medicinal Chemistry
Issue number5
Publication statusPublished - 1 Mar 2005

Scopus Subject Areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry

User-Defined Keywords

  • DNA
  • Noncovalent interaction
  • Protoberberine alkaloids
  • Spectrometry


Dive into the research topics of 'Spectrometric studies of cytotoxic protoberberine alkaloids binding to double-stranded DNA'. Together they form a unique fingerprint.

Cite this