DNA MOBILITY SHIFT ASSAY

Peter Cherepanov peter.cherepanov at uz.kuleuven.ac.be
Mon Oct 15 05:37:12 EST 2001


what about DnaseI hypersensitivity (in this case you will have to have an
idea which promoters are regulated by EM, because you will have to do
southern blot to detect change in Dnase sensitivity). For protocols - check
Methods in enzymology.
Folrmaldehyde or UV cross-linking may be also used, you cross-link all
transcription factors to DNA then IP them and do southern blot (in this case
you need to guess the factor and the promoter). This is better then mobility
shifts, because you see what is going on in vivo. This assay can be
quantitive. Again - check the Methods in enzymology series for protocols.

are you sure that there is any effect of EM?
Do they like EM?  How strong is the minimal exoposure to see an effect ?
have you got any mutants with different sensitivity? - that would be a good
start before any troubles with factors and promoters...

Peter

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