Skip to main content

Table 1 Kinetic parameters for the binding of PhaR to DNAs and P(3HB) on the 27-MHz QCM a

From: Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate]

Targetsb DNA sequencec k on d (10-4 M-1 s-1) k off c (10-3 s-1) K d e (10-7 M)
Control DNAf 5′bio-TCGTTTAACGAGCCCGTATTTTCCCCTCTACCTTTTAGAGGACACCTAAC-3′ 0.4 0.7 18
phaP1 promoterg 5′bio-GGCGCATTTCTTATTTGGTGCGCCGCAACAATTCCTATTTTA GGGGCGCC-3′ 6.0 ± 0.4 1.7 ± 0.4 3.2 ± 0.9
phaR promoterf 5′bio-TCACGCGTTTAGCCATAGCGGGCGCGGTA GACGAACAACAGCACGGCCGG-3′ 0.5 0.9 18
am-P(3HB)g   7.0 ± 3.8 -h -h
  1. a 10 mM HEPES buffer solution (pH 7.4) containing 150 mM NaCl and 0.002% Tween 20, 25°C. b 5′-biotinylated dsDNA immobilized on an avidin-covered QCM plate.
  2. Amorphous-P(3HB) thin film was prepared by casting chloroform solution (1.0 wt%) of the isotactic P[(R), (S)-3-hydroxybutyrate]. c The bold type indicates the DNA binding site of PhaR revealed by DNase I footprinting (4). d k on and k off were obtained from Eq. 4. e K d was calculated as k off/k on. f The data are from 2 independent experiments. g Amorphous P(3HB); the data are from 3 independent experiments. h K d value could not be calculated due to a negative k off value.