I would like to find a DNA specific sequence binding protein, which does not affect gene expression significantly and does not, ideally, exists in plant. Can anyone give me some suggest?
I have an interesting DNA fragment, which can bind some transcription factor. I would like to know which transcription factor can bind it in vivo. So I would like to fuse a special small DNA fragment, which can be bound by a known protein, before the interesting DNA fragment. Transfer both fusion DNA fragment and the known protein in Arabidopsis and I can use the known protein as prey to find the unknown TF binding on the interesting DNA fragment. So choose a suitable known DNA binding protein as the prey is most important.
Hi,
The idea sounds pretty smart but I doubt it will work as nicely as it sounds. You will have to consider lots of things like the orientation of your fusion and the length of potential spacers between you regulatory elements to allow for simultaneous binding. Also I am not aware of such a transcription factor.
Why don't you rather try to pull down your protein of interest in a protein lysate using e.g. a biotinylated oligo? It's not in vivo, but once you know what you are looking for you will have it easier to validate the binding.
Good luck,
Cindy
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