We repeated the digestion, ligation and transformations of a number of out parts before determining the reason behind why these weren't working.
At this point, we turned to using PCR to amplify some parts from plasmids we had been provided by Dr Alex Ninfa and Dr Susan Rowland, with gels showing bands of the correct sizes.
We purified these pieces and digested them, but subsequent ligations into the plasmid backbone pSB1C3 failed.