Another Gel shift misery!!

[folkguy]

Hi
I am working with transposable elements in mosquitoes. I am looking at the protein DNA binding. My problem with the gel shift is that the protein-DNA complex do not enter the gel , it just stick to the wells. I ahve changed buffer conditions and gel %age and acrylamide - bis acrylamide ratios upto 80:1. If someone had similar problem before and know how to solve it, please help me. I would appreciate it.
Thanks

[moleculardude]

Hmm.. thats weird. I would try very low percentage gels.

Try 6% and see if you get migration into the gel. I would first check your ladder to see if it is migrating into the gel.

Cheers and welcome to the forum!

[IronA]

I'm having the same problem as we speak. My positive control protein/DNA interaction is migrating into the gel, but my test with a different protein is not. gel= 6% 29:1 acrylamide bis.