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The engineered nucleases bind as a dimer to a target site, where they induce a DNA double-strand break.
Gapped motifs have been described for PTB (4 RRM domains, [ 124]) and the STAR family of RBPs (1 KH domain, but the proteins bind as a dimer, [ 125]).
According to Hasper et al. [ 26] there is evidence that although most zinc binuclear cluster proteins bind as a dimer, it seems that XlnR binds as a monomer - therefore, a Hill coefficient with h = 1 is used.
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SRs are a class of ligand-activated TFs; they include a ligand-binding domain which activates gene expression in the presence of specific sex or adrenal steroid hormones and a DNA-binding domain, which binds as a dimer to palindromic REs consisting of two half-sites each six bases long (Bentley, 1998; Bain et al., 2007).
Mature spätzle binds as a dimer to Toll, thereby inducing its dimerization at the plasma membrane.
NFI binds as a dimer, and its preferred binding sequence is a palindrome composed of two half sites TTGGCANNNTGCCAA.
The HD of Pax6 preferentially binds as a dimer to the palindromic DNA binding site: TAATYNRATTA (Y is C or T; R is A or G; N is any nucleotide), which is known as the P3 site.
CREB binds as a dimer to DNA and then recruits either CBP or p300 as a co-activator of transcription [22].
This arises because once the lexitropsin binds as a dimer in the minor groove, the cyclam is positioned beyond the backbone of the DNA helix.
NF-1 protein binds as a dimer to the dyad symmetric consensus sequence TTGGC N5 GCCAA on duplex DNA, although NF-1 can also bind specifically to individual half sites (TTGGC or GCCAA) with somewhat reduced affinity [24].
Under hypoxia, HIF-α is stabilized, translocates to the nucleus and binds as a dimer with the constitutive β-subunit and transcriptional co-activators to the hypoxia-responsive elements in the promoters or enhancers of its target genes (for review, see [18], [19], [20]).
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