Bantignies and Cavalli publish new DNA FISH protocol (in Cell paper on Hox Gene kissing). Recommend 15-25 kb for nicked translation: http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=5. Try using BACs as templates to start.
Also recommend FISH Tag DNA Orange Kit (A555) for better signal.
Try to visualize enhancer looping in activated and inactivated tissue — is TF binding affecting the looping rate or is the rate the same but the promoter modification different?