I am doing an experiment with a recombinant plasmid in CV-1 cells. I would like to engineer the response element of a small DNA binding protein into this plasmid in order to block an interaction I am investigating. Ideally this protein would have the following properties (in order of priority):
-it won't recruit other proteins
-it is already expressed in CV-1 cells
-its small (
It will be hard to find naturally occurring protein, which would not bring it's grandma and family. I don't know about any. But you could always use an artificial DNA-binder from ZFP or TAL family. ZFP for 9bp target will be only 10kDa and TAL will be 30kDa but it is easier to design. In that case, you won't be restricted on what sequence to use as a response element.
There are many online tools for TAL design, for example: http://www.e-talen.org/E-TALEN/. You could check others. I believe you could get all required plasmids at Addgene. This will be your most straight-forward way to what you are trying to do.
Like Dimitry, I would also recommend some sort of Endonucleases. Perhaps one with muted nuclease acitvity.
I'm not sure, you'll find anything endogeneous in CV-1 cells.
Best regards,
Yilmaz
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