No method is perfect, but our current favorite is to use Bernie
Weisblum's pDK101 vector. It has a special linker in the Nco I
site that when digested with XcmI leaves 1-base T overhangs. You
can directly clone fragments from Taq Pol amplifications, with an
efficiency advantage over blunt cloning. The reference is
Kovalic D; Kwak JH; Weisblum B.
General method for direct cloning of DNA fragments generated by the
polymerase chain reaction.
Nucleic Acids Research, 1991 Aug 25, 19(16):4560.
I agree with Dr. Bloksberg, though, that large fragments can be more of a pain.
aida at cgl.ucsf.edu