NFKb is a transcription factor that activates various genes. We have found the differential regulation of Pax6, as well as, NFkb in response to UV treatment under in vitro conditions. Can someone help me to design experiments that will help me to find out if NFkb is binding to the promoter of Pax 6 gene?
Thanks a lot!
Hi Bipasha,
there are some web tools but you can use this one:
http://bioinfo.lifl.fr/tfm-explorer/tfm-explorer.php
fred
You can do a Chromatin Immunoprecipitation or Promoter pull-down assay to confirm the same. Here is of the references that might be of help
Chaparian, R. R., & van Kessel, J. C. (2021). Promoter Pull-Down Assay: A Biochemical Screen for DNA-Binding Proteins. Methods in molecular biology (Clifton, N.J.), 2346, 165–172. https://doi.org/10.1007/7651_2020_307
Secondly, you can also do an in-silico molecular docking before the in-vitro experiments.
Best wishes,
Bipasha B
ClusPro is software that can help you in finding if they can bind via generating a binding model for them.
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