After BP reaction I get quite few normal sized colonies, which indicates that the reaction worked. However, when I do double restriction digestion on the miniprepd plasmid from transformed bacteria I do not get the right size bands.

My construct is 4.2 kb long and after BP with pDONR223 the resulting entry vector should be 7kb long. However, when I do a digestion I always see bands around 3kb. I thought it might be the donr vector recombining with itself and yes that was right. Restriction digestion confirms that 3kb band is pDONR223 recombining between its attP sites.

Has anybody else have this problem before? My insert is human TONSL orf, which contains ankyrin, TPR and LRR repeats.