I'm trying to produce a high resolution restriction map of a cloned 10kb piece of archaebacterial DNA. I've tried a variety of enzymes on plasmid DNA isolated with a miniprep kit, but I'm constantly getting partial cutting with most of the 20 enzymes I'm using. I've tried different amounts of DNA in the digest, and digested for differing times, but to no avail! It happens even for non-methylation sensitive enzymes.Can anyone offer any advice as to how to prevent partial cutting, otherwise I'm going to pull my hair out!
Thanks a lot!