Hello. I have a strange problem. I inserted a Flag sequence into pMX retroviral vector. Now this new pMX-Flag vector has a hard time to digest (only about 20% gets digested) with any restriction enzyme in the polylinker while the old pMX cuts beautifuly. I sequenced the new pMX-Flag clones and there is no problem. I have never heard about such a problem. I am using qiagene miniprep plasmids - can they be dirty and so not cut? Original pMX is a maxiprep.
Thank you for suggestion since I am clueless.
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