Has anyone tried DNase footprinting on single stranded DNA or heteroduplex DNA? It is said that DNase is 500 times less active on single stranded DNA than double stranded DNA.
I wanted to perform footprinting on heteroduplex DNA (DNA harboring bubbles/ loops). But given that DNase is less active on ssDNA, it would become difficult to appreciate the footprint as DNase would act differentially on ss and ds region on the same DNA.