The binding specificities of five mouse Fkh TFs, Foxa2, Foxj1, Foxj3, Foxk1 and Foxl1 (Robasky and Bulyk, 2011) were used to identify three Fkh-binding sites within a previously characterized mesodermal enhancer from the Ndg gene (Philippakis et al., 2006) (Fig. 1; supplementary material Table S1).
Using in vivo studies together with documented binding specificities of three transcription factors known to have a role in the regulation of respiratory genes (the Hap complex, Cat8 and Mig1), it was possible to correlate the up-regulation of all but 18 of the 146 genes induced by a factor ≥2.0 with the presence of one or more of their binding sites.
The trained SVR models do not directly predict PFMs, but the similarity of the DNA-binding specificities of two TFs.
The carbohydrate binding specificities of the two CRDs are quite different and would be expected to show preference for different sets of ligands.
The fragment approach was then used to analyze and understand the binding specificities of the nine ligands.
The crystal structure of the P dimer of a GII-4 norovirus (VA387) bound to types A and B trisaccharides has elucidated the A/B binding site on the capsid but did not explain the binding specificity of the two antigens.
To test the binding specificity of the two baits, pairwise Y2H assays were performed by co-transforming them in yeast with the prey proteins CKS1, CYCP1, CYCP6, dsCYC7 and dsCYC2, which was previously described as an interactor of CDKA1 [ 28].
In a fourth selection set, we tested the partitioning efficiency and binding specificity of our three proteins' aptamers, as well as two suspected background binding sequences, to eight targets running serially.
We used this technology to characterize the binding specificities of OsSMF1 and identified three DNA-binding motifs for this transcription factor, including the GCN4 (TGA(G/C TCA), ACGT (CCACGT(C/G)), and ATGA (GGATGAC) motifs (Figs. 2 and 3).
The binding specificity of the three antibodies tested was the same as in the SDS PAGE.
