I was given a PCR product with BamHI sites conveniently located near, but not at, the ends:

BamHI BamHI

I then cloned the BamHI fragment into pUC19 as follows: First I digested the pUC19 and the PCR product with BamHI so they would have complementary ends. Next I purified the two pieces I wanted to combine together by gel electrophoresis. Finally I ligated them together.

But the problem with cloning into a single site this way is that the DNA has a 50:50 chance of inserting in either orientation.

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