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This makes sense have reading what your comment. I overlooked this and just assumed the GATC was a mutation that allowed the restriction enzyme to work on the mutant only.
it makes even more sense when looking at "numerous small fragments." Methylation is truly the obvious answer here in retrospect.
DNAse can also cause a change in base by breaking down dna at the GATC sequence?
@bgiri Had the same reasoning - according to wiki, DNase catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA.