Despite using the same amount of DNA why do you get so many

Despite using the same amount of DNA, why do you get so many more colonies for a reaction that has no cut vector or cut insert with white/blue screening?

Solution

When the vector is single cut it will easily self ligate in the vector only control tube ( this self ligation occurs much more efficiently than does the vector to insert ligation). In the vector + insert tube, the vector will still self ligate. However, a portion will also ligate to the insert on one side where the ends are compatible but will be unable to ligate on the other side where the ends are incompatible. This will essentially kill the efficient self ligation of the plasmid. Therefore, you will see more colonies for the vector only plate than you will see in the vector + insert plate. If there are some double cut vector in the tube then you may also get vector + insert recombinants and you may be able to find these if you test colonies on your vector + insert plate. The percentage will depend on the proportion of double cut vector that was in the tube and if one enzyme did not cut at all then you will have zero recombinant colonies.