Transfer the aqueous phase to a sterile eppendorf tube. Microfuge at 4 degrees C immediately for 30 minutes. If you suspect low yields place samples on dry ice for 10 minutes prior to spinning. Decant the supernatant immediately and vacuum dessicate or lay tube on its side to dry the DNA pellet for 15 minutes. Run gel 4-8 hours at 80 volts until the desired separation is obtained.
Vector is now ready for ligation.
Insert Preparation Digest 10-20 ug of insert DNA with the appropriate enzyme in a 100 ul volume. Remove 5 ul for a test gel. This can be achieved by taping several wells together. Be certain that the taped comb clears the bottom of the gel bed. Also prepare a mini-gel to run a 5 ul aliquot to verify complete digestion and running time to obtain desired separation.