footprinting & gelshift - (Jun/28/2004 )
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?
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.