I am trying to clone a 1000 bp fragment, obtained by SOEing PCR into a vector. After restriction, the PCR product looks fine on a gel. However, mysteriously after ligation, transformation and test restriction the fragment is not 1000 bp, but either 400, 500, 750, 900 or so. All these fragments were sequenced and they represent smaller or bigger parts of the desired 1000 bp one, however I can never get 1000. Has anybody got an idea as to what's going on with this ligation? I would appreciate your help on this issue.
Edited by doomo, 23 January 2012 - 03:27 PM.