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Fig. 3. Ci binds the D-h activation element, while Brk and Mad bind the
repression element. Binding of the Ci DNA-binding domain to the Ci1 site in
HHRE (lanes 1-7) and binding of full-length Brk or GST-N-Mad protein to the
CMB element (lanes 8-27) were tested by EMSA. Sequences of Ci1 site wild-type
(Ci1 wt), CMB site wild-type (CMB wt) and the following mutant probes are
shown below: Ci1 site mutant (Ci1 mut), Brk site mutant (Brk mut), Mad site
double-mutant (Mad dmut), Mad site single-mutant (Mad smut), CRE mutant (C
mut), Mad2 site mutant (M2 mut), Brk/Mad2 site mutant (BM2 mut) and Mad1/Mad2
mutant (MM mut). Putative binding sites are underlined on the wild-type
sequences. Lanes 1-7, sequence-specific binding of Ci protein to the Ci1 site;
lane 1, Ci1 wild-type probe and no protein; lanes 2-6, Ci1 wt probe + Ci
protein and no competitor (lane 2), 10x specific competitor (Ci1 wt
oligo) (lane 3), 100x specific competitor (lane 4), 10x
nonspecific competitor (Ci1 mut oligo) (lane 5), and 100x nonspecific
competitor (lane 6). Lane 7, Ci1 mut oligo + Ci protein; lanes 8-14,
sequence-specific binding of Brk protein to the CMB element; lane 8, CMB wt
probe and no protein; lanes 9-13, CMB wt probe + Brk protein and no competitor
(lane 9), 10x specific competitor (CMB wt oligo) (lane 10), 100x
specific competitor (lane 11), 10x nonspecific competitor (Brk mut
oligo) (lane 12), 100x nonspecific competitor (lane 13). Lane 14, Brk
mut probe + Brk protein; lanes 15-22, sequence specific binding of Mad protein
to the CMB element; lane 15, CMB wt probe and no protein; lanes 16-22, CMB wt
probe + Mad protein and no competitor (lane 16), 10x specific competitor
(CMB wt oligo) (lane 17), 100x specific competitor (lane 18), 10x
nonspecific competitor (Mad dmut oligo) (lane 19), 100x nonspecific
competitor (lane 20). Lane 21-22, Mad protein + Mad dmut probe (lane 21) or
Mad smut probe (mutation is in Mad2 site) (lane 22). Lanes 23-27, Brk protein
binding to CMB wt probe (lane 23), C mut probe (lane 24), M2 mut probe (lane
25), BM2 mut probe (lane 26) and MM mut (lane 27).
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