Request info. on Gel Bandshift (Retardation ) Assay

[Waleed Khan]

I am borrowing this person's ID to post my problem.
I am a summer student doing research in the department of nephrology/
immunology.  I am currently having difficulties running a bandshift assay.
Instead of seeing sharp and distinct bands of protein and DNA complex,
I am getting a smear.

We are running an 80:1 acrylamide to bisacrylamide, 5% gel.
The protein we are using is from a nuclear extraction of Jurkat and 
peripheral blood lymphocytes.  The method of nuclear extraction is followed
according to Dignam's protocol.  Our probe was originally synthesized on
a DNA synthesis machine and purified via a trityl column.  We are attempting
to purify our probe via cloning and/or an agarose gel.  I would like 
suggestions on improving this experiemental method.

If anyone can help me (or direct me to a more appropriate user group), 
please post a follow up article or email me directly via this ID.

Sophia
khan at eigen.ee.ualberta.ca
U.Alberta, Edmonton