Interaction study between double-stranded DNA and berberine using capillary zone electrophoresis.
Two non-self-complementary 17-mer double-stranded DNA (dsDNA) with four different central base pairs were designed to systematically investigate the binding affinity and sequence specificity of berberine with dsDNA by capillary zone electrophoresis (CZE). The data analysis with the Kenndler model proved only low affinity between dsDNA and berberine and suggested some weak binding preference of berberine for AATT-containing to GGCC-containing dsDNA. The binding constant, Ka, between berberine and dsDNA(AB) was about (1.0 +/- 0.7) x 10(3) M(-1). In addition, the separation of single-stranded DNA (ssDNA) from dsDNA under simple electrophoretic conditions enabled CZE to be a potentially alternative tool to check the extent of DNA annealing, which is usually done by the time-consuming and labor-intensive slab electrophoresis.
Wu
Juan-Fang
JF
Department of Chemistry, Tsinghua University, Beijing 100084, China. jf-wu03@mails.tsinghua.edu.cn
Chen
Ling-Xin
LX
Luo
Guo-An
GA
Liu
Yong-Suo
YS
Wang
Yi-Ming
YM
Jiang
Zhi-Hong
ZH
D001483:Base Sequence; D001599:Berberine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D017931:DNA Primers; D019075:Electrophoresis, Capillary / Q000379:methods*
D017931:DNA Primers; D001599:Berberine; D004247:DNA