Well, it is possible that your sites are too close to the end of your fragments. To have an efficient cut of EcoR I when this site is close to the end, you have to have this sequence: CCGG GAATTC CGG For BamHI, it is:CGC GGATCC GCG Dimitri Harmegnies ldewit at ben.vub.ac.be Dept. of Virology Institut Pasteur de Bruxelles 642 rue Engeland B-1180 Brussels, Belgium