The purification of large DNA constructs from bacteria such as BACs, PACs, P1s, and cosmids can be troublesome. Not only are these constructs usually present at low copy number compared to plasmid DNA, but downstream applications usually require a higher level of purity. In addition to their extensive offering of plasmid purification kits, Qiagen has produced a kit for purifying large constructs. The kit comes with all the buffers, solutions and columns you need to purify your DNA; a handbook is also included which very clearly explains the protocol and provides a detailed background of the kit, which is somewhat lacking with most companies.
After pelleting bacteria grown according to instructions, the kit starts with standard alkaline lysis (as performed for a plasmid prep) and the resulting lysate is combined with ATP-Dependent Exonuclease. This digestion removes genomic DNA. Following the digestion step, construct DNA is bound to a column containing Qiagen’s anion-exchange resin. The column-bound DNA is washed to remove impurities and then the DNA is eluted and precipitated.
With a number of different BAC constructs, I have successfully obtained higher yields with this kit than with common plasmid prep methods. The DNA was also of good quality as it was transfectable and produced recombinant virus. I would recommend sticking to the protocol and not deviating from what is suggested in terms of culture volumes, incubation times, etc.
In conclusion, this is a very useful kit for the purification of high quality/yield large construct DNA.