STAT transcription factors bind to similar DNA sequences, and the similar DNA binding specificity of various STAT transcription factors, such as STAT1, STAT5A/5B, or STAT6, have been experimentally proven [56].
For rational design of selective RNA binders, detailed knowledge of structure affinity relationships between RNA and small molecules is required, as well as analysis of the binding specificity of various RNA sequences.
Recently, several high-throughput techniques, such as protein microarray, phage display and SPOT synthesis, have been developed, which can detect the binding specificity of various modular domains.
By contrast, the nature of nucleotides at position N3 and N12 can either enhance or reduce the binding affinity, which supports their contribution in determining the binding specificity of various ERFs to target promoters.
Site-directed mutagenesis revealed that the nature of the flanking nucleotides can either enhance or reduce the binding affinity, thus conferring the binding specificity of various ERFs to target promoters.
In particular, the data clearly demonstrate that the nature of the nucleotides at position N3 and N12 can have different and sometime opposite effect on different ERFs, thus suggesting that these bases contribute to the binding specificity of various ERFs to target promoters.
The carbohydrate-binding specificity of various purified galectins has been studied extensively and interpreted in terms of the three-dimensional structures which have been determined for CRDs derived from galectin-1 (Gal1), galectin-2, Gal3, galectin-7, and Gal3ctin-10 (see Leffler et al. 2004 for an overview).
Affinity gel electrophoresis was performed to test binding specificities of the GFP_CBMs to various soluble polysaccharides (HEC, icelandic moss lichenan, carob galactomannan, beechwood xylan, and wheat flour arabinoxylan) [ 40, 106].
In order to test the histone binding specificities of other plant MRG chromodomains, we analyzed the binding affinities of two plant MRG chromodomains to various histone peptides via isothermal titration calorimetry.
While microarrays of immobilized glycans have been successfully used before for the determination of binding specificity of HAs from various influenza A virus sources, we prefer microarrays of glycans (glycolipids) in the fluidic supported lipid bilayer (SLB) environment to better mimic the dynamic environment of cell membrane.
