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For a given remodeling reaction time, the farther the Gal4 binding site is separated from the 601NPE, the lower the probability of detecting a remodeled nucleosome that is repositioned to the other side of the Gal4 binding site.
As shown in the new Figure 4 source data 1 (right column), in the absence of ATP, SWI/SNF does not result in Gal4DBD dissociation, even when the Gal4 binding site is separated by 10 bp from the 601NPE.
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Lac repressor binding site was separated from the 601NPE by 10 bp.
Therefore, we have conducted an additional experiment on a template where the Gal4 binding site was separated from the 601NPE by 24 bp.
Two binding sites are separated into two disjoint enriched regions by PICS, whereas MACS [5] combined these two sites into a single region.
A Monte-Carlo assessment further confirmed that the enrichment of paired PPARγ/RXR binding sites is significant at FDR<0.05 when these bona fide individual binding sites are separated by <300 bp (Figure 3C).
The crystal structure of the fiber-knob protein shows that the three known sialic acid binding sites are separated by distances of about 10 Å.
The binding sites are separated by 30 or 29 nucleotides in the promoters of E spl) genes of Drosophila melanogaster and higher vertebrates, respectively [ 33, 34].
The active sites of each noncrystallographic pair of subunits (A B and A′ B′) are connected by an internal cavity or tunnel, and the substrate binding sites are separated by about 35 Å.
Alternatively, after linker ligation, the DNA could be redigested with an endonuclease that cuts within the flanking plasmid DNA so that the primer binding sites are separated on different molecules (see [257]).
In this case, the reaction mixtures of limiting antibody and excess total PSA were only seven seconds old and far from equilibrium when the antibody molecules with unoccupied binding sites were separated from the reaction mixture and quantified using the immobilized PSA.
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