Currently I am trying to clone an attB PCR product into gateway pDONR221. After performing the BP reaction I got some few clones which I checked by M13 PCR and they seemed to be positive. However, sequencing revealed that quite a substantial part of the gene is missing, i.e. starting with a PCR product of almost 600 bp, I end up with only a bit more than 300 bp inserted into the vector.
Subsequently I cloned the attB PCR product into pGEM, checked it by sequencing and got exactly what I expected: my 600 bp sequence with the attB sites on both ends. So I think it is a problem with the BP clonase reaction?
Has anyone encountered similar problems? Any ideas?