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RITA could not displace MDM2 binding in these experiments leading to the conclusion that RITA does not bind the N-terminus of p53 [ 54].
Non-specific binding in these experiments comprised less than 5% of total counts.
A dose of 75 μ M NS-398 was used for reporter assays in order to maximise the activation of NF- κB DNA binding in these experiments.
Membrane bound radioligand was separated by filtration through Whatman GF/B filters soaked in 0.3% polyethyleneimine on a Brandel cell harvester, and retained radioactivity was quantified using a gamma-counter (Packard Cobra II, Perkin Elmer, Waltham, MA, U.S.A .. Non-specific binding in these experiments comprised less than 5% of total counts, and was subtracted from the data.
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Wild type Zif268 (displayed on phage) was used as control against its cognate 9-bp binding site in these experiments (Figure 1C).
In the revision, we have modified the experimental protocol to avoid saturating OPD signals, so that we accurately measure total CTB binding in this experiment.
Finally, the performance of the peak detection algorithms was evaluated with respect to regions that were confirmed in independent qPCR experiments to be bound by the particular transcription factor (true positives) as well as regions that did not show binding (true negatives) in these experiments.
The ZF DNA-binding domain used in these experiments was ZF43-8 (ref. 24).
To measured binding affinity, competition binding was performed with 0.6 nM [H]granisetron (close to Kd for this ligand) for 120 min. In these experiments, binding was performed at 19°C to inhibit receptor endocytosis.
The significant results identified by this analysis (* p < 0.05; ** p < 0.001) are indicated in Figure 4. Our operational assumption is that the binding of opsin by arrestin in these experiments is at (or near) saturating levels, because experiments using both 2 and 5 μM arrestin show almost identical results.
This indicates a high degree of non-specific binding in microarray experiments when using longer oligo- or polynucleotides and RNA as target molecule.
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