It seems to me that the eletrophoresis failed to seperate the free probe from
DNA-protein complex. 400 bp probe is a lot big. I quite agree with the
suggestion of adjusting your gel concentration or Acr/Bis ratio. I think it
might be easier to use the probe only to optimize the gel first, at least to
let the free probe run to the bottom. You don't need to label the DNA. Instead
you can use EB to stain the DNA. To my personal opinion, I think 5% gel is not
the best choice. Gernerally I believe 3%
