Gel Shift Question

Steve Rodems smrodems at
Tue Mar 8 09:27:28 EST 1994

I have started to do gel shift experiments and I have a question about
doing competition studies.  My probe is about 30bp.  Now, in a competition
study I use cold 30bp DNA as a specific competitor and linear BS/KS+ as
non-specific competitor (ie, should not compete off my specific complex). 
If I want 100-fold molar xs of competitor I can add 100ng cold 30bp DNA per
1 ng 30bp probe.  My question is how much BS do I use?  100-fold molar xs
of BS actually has about 100x as many 30-bp sites since each molecule of BS
has about 100 30bp sites (that would actually be a 10,000 molar xs of 30-bp
sites if I'm thinking about this right).  So, what is the conventional way
to do this, molar xs of a whole piece of DNA or molar xs of available x-bp
binding sites?

Steve "Some day I will get the hell out of Wisconsin" Rodems

"Then I am here for the Lee family renioun ... shur-wajo-shur"

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