I am trying to set up for DNase I footprinting. I use 50ng of PCR product (app. 500 bp) labelled with 5' FAM. I am using RQ1 enzyme from promega. I am using 0.1U of DNase I with incubation on thermocycle at 25C for 3-4 minutes. I tried two different targets H1.2 and E2F1 to rule out hyposensitive region phenomenon. Yet I am observing same pattern. I appreciate if anyone has suggestion how I can optimize my limited DNase I digestion.
Please refer to the attached image, yellow region is indicated region for the least DNase I digestion.
Thank you,
Regards,