hi! All

I am analyzing a transcription factor for its domains, I want to test if one motif about 12 residues long helps in DNA binding directly by making contacts with DNA or by affecting the the DNA contacting domains. Please let me know if there is a way to differentiate between these two possible functions. And if there is an example in literature of any such similar instance please let me know.

Any information/input -much appreciated

thanks a lot

Rnn

Your best guess is to start looking for the scores of classical DNA binding motifs. Domains affecting, but not pertaining to DNA binding are, obviously, different. They generally just affect conformation to allow/inhibit DNA binding.

The gold standard to determine the actual binding, however, are crystallization studies. Alternative to that one could try to isolate the DNA-binding domain (plus possible dimerization domain) and demonstrate binding by DNAse protection assays or EMSA.