My colleagues and I have an experience of successful cloning into various plasmid vectors. We noticed that it is hard to clone some inserts into one vectors, while the same inserts can be readily cloned into other vectors. In our hands, one of these hard-to-clone vectors is pEGFP-N1. With various cloning strategies my colleagues and I obtain a very few colonies, which often do not contain the vector with the insert. The same inserts can be easily cloned in other vectors. What can be wrong with pEGFP-N1? Did you have the same problems with some vectors? Did you solve similar problems?