Non specific carrier DNA in gel shift assays.

Antonin Tutter atutter at
Sun Oct 4 00:32:22 EST 1998

>A few weeks ago I posted a message concerning gel shift bands.  I have
>tried the various suggestions and was able to get a very prominent band
>using salt and non-ionic detergent in the absence of poly di/dc.  I have
>since added the poly di/dc and found that this band dissappears.  My
>concern is when using this non-specific carrier DNA, how is it able to
>remove such a prominent band(that seems to be specific).  It seems as
>though the carrier DNA may be affecting my assays.  Thank You
>Ezra Schildkraut
>University of New Mexico

I remember posting a reply to your original question.  poly(dIdC) is a
non-specific competitor, however if the band you suspect to be specific is a
major-groove-binding protein, the dIdC may be outcompeting your probe.  dIdC
generally mimicks a major groove like GC-rich sequences do.  Try switching
to poly(dAdT) and see if that also outcompetes your probe.  If so, your band
is probably not specific.  

good luck,

Antonin Tutter
Salk Institute for Biological Studies
10010 N. Torrey Pines Rd.
La Jolla, CA  92037
email:  atutter at

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