Hi,
I have a question about in vitro analysis of DNA binding protein. I
want to quantitate the Kd for a viral transcrition transactivator with
it's target DNA sequence. Problem is this protein can form dimer,
trimer or tetramer on the DNA via protein-protein interaction. So there
are up to 4 shifted bands in the gel-shift assay. I check out some
reference about the methodology of Kd assay but all of them require that
the binding reaction obey two-molecule reaction model, that is P+D =
PD.
Can anyone tell me how to get the Kd for DNA binding protein that can
multimerized and give me some reference if you can. Can I simply count
all shifted band as [PD]? Thank you very much in advance!
Regards!
Yibin Kang
Duke Univ. Med. center, CMB program
