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A crucial question when carrying out binding experiments for high-affinity interactions is whether the reaction has come to thermodynamic equilibrium.
Reviewer #2: 1) The binding experiments for the Nedd4L-AMOT interaction are carried out using a variety of constructs to localize binding determinants.
Firstly, we have carried out SPR binding experiments for the interaction of wild-type Norrin with Lrp6, and we have added these data to the manuscript.
It was notable that IC50 values for the Gi-mediated function gene transcription responses were generally much lower than the KD values obtained in binding experiments for all agonists.
We first compared how replicate binding experiments for the same TF differ among distinct C57BL/6J individuals by plotting ChIP intensities against each other in an X-Y scatterplot.
In contrast to the conditions adopted for binding to PC-3 cells, binding experiments for U87-MG cells were conducted in binding buffer (50 mM Tris, pH 7.4, 100 mM NaCl, 2 mM CaCl2, 1 mM MgCl2, 1 mM MnCl2, and 1% bovine serum albumin) for 2 h at 25 °C prior to washing twice using cold binding buffer followed by reading the NIR signal of the entire plate.
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Such insoluble proteoliposomes cannot even be applied to receptor-binding experiments for subsequent affinity purification of the bound complexes.
Figure 7a shows the results of DNA-binding experiments: for Ssh10b, 370 ng of supercoiled plasmid DNA were visibly shifted at protein quantities greater than 0.7 µg.
Figure 7b shows the results of RNA-binding experiments: for Ssh10b, 1.1 µg of total RNA from Escherichia coli DH5α were visibly shifted at protein quantities greater than 1 µg.
The arrangement of the XPC promoter places the elements 8 nucleotides apart, identical to EGR1, and there is no evidence from the DNA-binding experiments for simultaneous occupation of the sites.
To address this possibility, we repeated peptide-binding experiments for SMN D44V in the presence and absence of 0.05% NP40, both at 25°C and at 4°C.
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