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Korean Chemical Society (대한화학회)
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DNA Binding Mode of the Isoquinoline Alkaloid Berberine with the Deoxyoligonucleotide d(GCCGTCGTTTTACA)2

  • Park, Hye-Seo (Department of Biochemistry, Protein Network Research Center, Yonsei University) ;
  • Kim, Eun-Hee (Magnetic Resonance Team, Korea Basic Science institute) ;
  • Sung, Yoon-Hui (Department of Biochemistry, Yonsei University) ;
  • Kang, Mi-Ran (Department of Biology, Protein Network Research Center, Yonsei University) ;
  • Chung, In-Kwon (Department of Biology, Protein Network Research Center, Yonsei University) ;
  • Cheong, Chae-Joon (Magnetic Resonance Team, Korea Basic Science institute) ;
  • Lee, Weon-Tae (Department of Biochemistry, Protein Network Research Center, Yonsei University)
  • Published : 2004.04.20
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Abstract

The ability of protoberberine alkaloids, berberine and berberrubine, to act as topoisomerase II poisons is linked to the anti-cancer activity. Minor alterations in structure have a significant effect on their relative activity. Berberine, which has methoxy group at the 19-position, is significantly less potent than berberrubine. Several observations support non-specific binding to HP14 by the berberine: (i) nonspecific upfield changes in $^1H$ chemical shift for protons of the berberine; (ii) the broadening of imino protons of HP14 upon binding of the berberine; (iii) very small increases in duplex melting temperature in the presence of the berberine. Our results reveal that substitution of a hydroxyl group to a methoxy group on the 19-position, thereby converting the berberrubine to the berberine is associated with a non-specific DNA binding affinity and a reduced topoisomerase II poisoning. The presence of a bulky 19-methoxy substituent decreases intercalating properties of berberine and makes it inactive as topoisomerase II poison.

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