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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 25, Number 4
BKCSDE 25(4)
April 20, 2004 

DNA Binding Mode of the Isoquinoline Alkaloid Berberine with the Deoxyoligonucleotide d(GCCGTCGTTTTACA)2
Hye-seo Park, Eun Hee Kim, Yoon-Hui Sung, Mi Ran Kang, In Kwon Chung, Chaejoon Cheong, Weontae Lee*
Berberine, Topoisomerase II poison, DNA binding, NMR
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.
539 - 544
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