first time running DNA polyacrylamide TBE gel - (Aug/20/2014 )

This is my first time running nucleic acids on a polyacrylamide TBE gel. I first cast a polyacrylamide gel using our BioRad equipment that we usually use for Westerns (1X TBE, 10% 29:1 acrylamide, 0.1% APS, TEMED), loaded my samples, and ran at 130 V for 70 minutes in 1X TBE. I noticed that my bromophenol blue marker only migrated one-third of the way down the gel. Could this be due to using loading dye I usually use for TAE agarose gels (1X TAE, Ficoll 400)? Should I make another loading dye with 1X TBE for these gels? Will my samples still migrate okay? Thanks.

yes, you should use loading dye with tbe. the tae may have an effect on migration.

If I am using BioRad containers, do I need to pre-electrophorese the gel?

The bromphenol migrates also depending on the gel density, different on 1%, 2% agarose gel. So I would expect it to migrate very differently on polyacrylamide gels.
And you shouldn't use different buffers in loading and in gel. 

labstud4 on Thu Aug 21 16:30:36 2014 said:

If I am using BioRad containers, do I need to pre-electrophorese the gel?

it's always a good idea to pre-run a continuous buffer gel like the one you're using (it's not a good idea when running discontinuous gels), it "cleans" the gel.