ssDNA smear during gel shift - (Oct/31/2005 )
this is the first time i ran a native polyacramide gel to detect binding between different sized ssDNA and my protein, however unlike the distinct bands i expect to see of the ssDNA, a smear is formed, i have no idea why this is happening...
i used a tris-acetate buffer pH7.4 as running buffer at 4C on a 9% gel (same as running buffer)
have you looked at pix of others' gel shifts?
You usually get a smear for your oligo; how big of a smear are you talking here? could you enclose a pic for us?
the smear is from the xylene cyanol marker to around the bromophenol blue marker
and i was using a 90mer. the 9% native page was in a ratio of 37.5:1 bis:acryamide.
what about your other bands? were they smeary too? what is your glycerol concentration in the sample?