Synthesis, DNA-binding affinities, and binding mode of berberine dimers

Yong Qin, Ji Yan Pang, Wen Hua Chen*, Zongwei CAI, Zhi Hong JIANG

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

65 Citations (Scopus)


Six novel berberine dimers (3a-f) were synthesized in 37-84% yield from the reaction of berberrubine (2) with dihaloalkanes of varying lengths from two to seven carbons. Their interactions with calf thymus (CT) DNA and three double helical oligodeoxynucleotides, d(AAGAATTCTT)2, d(AAGCATGCTT) 2, and d(TAAGAATTCTTA)2, were investigated by means of fluorometric titration and ethidium bromide (EB) displacement experiments. Compared with the monomeric parent berberine (1), these dimers' DNA-binding affinities increased up to approximately 100-fold, suggesting a cooperative interaction of the two berberine subunits in the molecules. Furthermore, these dimers linked by different spacers show a prominent structure-activity relationship when bound with oligodeoxynucleotides. The relative binding affinities are in the order of 3b > 3a > 3c > 3d > 3e > 3f with d(AAGAATTCTT)2 and d(TAAGAATTCTTA)2, and 3b > 3c > 3a > 3d > 3e > 3f with d(AAGCATGCTT)2. Dimer 3b, linked with a propyl chain, exhibits the highest binding affinity. This suggests that a propyl chain may be the most suitable spacer to bridge the two berberine units for DNA binding. Spectrophotometric titration and competitive EB displacement of berberine (1) and dimer 3b indicate that both berberine and its dimers form intercalating complexes with duplex DNA. A larger redshift, a stronger hypochromic effect, and a much higher EB displacement ratio, observed in 3b, indicate that the dimer is in more intimate contact with DNA than berberine. In addition, no obvious binding of canadine (4), a hydrogenated product of berberine, with CT DNA was observed, suggesting critical roles of the quaternary ammonium cation and planar structure in the DNA-binding of berberine.

Original languageEnglish
Pages (from-to)25-32
Number of pages8
JournalBioorganic and Medicinal Chemistry
Issue number1
Publication statusPublished - 1 Jan 2006

Scopus Subject Areas

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

User-Defined Keywords

  • Berberine dimer
  • DNA-binding
  • Ethidium bromide displacement
  • Fluorescence spectrometry
  • Intercalation


Dive into the research topics of 'Synthesis, DNA-binding affinities, and binding mode of berberine dimers'. Together they form a unique fingerprint.

Cite this