You are only limited here by the resolution of the gel you intend to use to look at the footprinted DNA. If you are using radioactivity, you are probably using traditional urea slab gels which aren't very effective above 300 bases, but can go to 500-600 bases. It is best to run the footprints labeled at both ends (in parallel) and therefore in order to see the same regions from both ends your product has to be within the resolution of the slab gel.

Thanks Prescott Deininger. This was helpful

Hey Chad, DNase footprinting depending on what protein you are footprint you will get different sized products. Close to about 100 would be a good size to restrict yourself to. THis way you can get the small transcription factors too.

Thanks for the input Jude