I'm developing a protocol that includes a step where DNA needs to be cut
randomly, leaving blunt ends. I initially digested the DNA with DNase I
and cut out the band corresponding to linear DNA. When I sequenced my
final clones, it turned out that many of the termini had been chewed
Someone else in the lab tried digesting with DNase I to get nicked DNA.
This step was followed by treatment with S1 to break the nick.
Sequencing again revealed that some sequence had been deleted.
Does anyone have any suggestions? If so, please let me know.
OVanHam at UWO.CA