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footprinting & gelshift

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#1 dreamcatcher



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Posted 28 June 2004 - 01:51 AM

In footprinting and gelshift, usually we will add poly(dI-dC)¡Ppoly(dI-dC) to block non-specific binding proteins. Poly(dI-dC)¡Ppoly(dI-dC) acts as nonspecific competitor.
I have checked the Amersham website, and it says that
"The synthetic polymer poly(dI-dC)¡Ppoly(dI-dC) is useful in DNA-binding protein studies (1-4) because it is sufficiently like cellular DNA to soak up non-specific binding proteins, yet sufficiently different to avoid inadvertent binding of the specific proteins of interest."
But why Poly(dI-dC)¡Ppoly(dI-dC) can bind with other non-specific protein?

#2 pcrman



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Posted 28 June 2004 - 08:52 AM

Nonspecific competitor DNA such as poly(dI•dC) or poly(dA•dT) is used in DNA-protein interaction assay such as footprinting, gel-shifting to minimize the binding of nonspecific proteins to the labeled target DNA. These repetitive polymers provide an excess of nonspecific sites to adsorb proteins in crude lysates that will bind to any general DNA sequence.

To maximize its effectiveness, the competitor DNA must be added to the reaction along with the protein prior to the labeled DNA target.

#3 LT Dusty

LT Dusty


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Posted 21 May 2009 - 11:05 AM

I have a question.....I'm trying some DNase 1 footprints and I can't get the DNA into the gel, it is a 5% acrylamide, 7.5M urea gel, and the running buffer is 1X TBE. Does anyone know why the DNA won't enter the gel. The dye markers are migrating funny as well. The bromophenol blue marker just disappears halfway through the run...not that it matters since the DNA won't run either. Thanks for any help.


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