QuickClean 5M Gel Extraction Kit From GenScript Corporation

The term “DNA cleanup” almost always refers to the removal of unwanted components from a reaction prior to using the DNA of interest in a subsequent procedure. These unwanted components can include salts, nucleotides, primers, and enzymes. When the components targeted for removal are small molecules or proteins such as these, a spin-column based cleanup kit is the method of choice as it is one of the easiest and most effective techniques around. These kits work by binding DNA of a specified size range and allowing everything else to be washed through. The size range of the DNA that is most effectively bound is chosen so that the cleanup kit can be used to purify DNA amplicons from PCR reactions. Hence, small DNA oligos, like primers, won’t bind, but amplicons of at least ~100 bp will.

While this works fine for most PCR reactions, there are many instances where an alternative cleanup procedure is warranted. For example, the separation of a 500 bp insert from a 2 kb plasmid following a restriction digest cannot be accomplished with a PCR cleanup kit as both species of DNA will bind to the spin column. In a case such as this, the easiest approach is to run the reaction on an agarose gel, excise the DNA band of interest, and elute the DNA from the gel. Although this procedure can certainly be accomplished with off-the-shelf reagents, there is an impressive assortment of kits available to simplify the task. I recently used GenScript Corporation’s QuickClean 5M Gel Extraction Kit to purify a ~700 bp DNA fragment from an agarose gel and found it to be very effective, in addition to being one of the least expensive kits around.

The QuickClean Kit protocol is essentially identical to that of the leading brands and includes adding a binding solution to the excised agarose gel piece containing the DNA of interest, solubilizing the agarose by incubation at 50°C, adding isopropanol to the mixture, and spinning it through a spin column. After washing through the unwanted components with another spin or two, the target DNA is eluted into a clean tube. In my case, the recovery was over 80% and the 260/280 ratio was 1.7. Sequencing the fragment yielded 621 bp of clear read; essentially the entire fragment.

Some other relevant details of the QuickClean Gel Extraction Kit include a capacity of 20 µg DNA per spin column, a binding size range of 70 bp to 10 kb of single- or double-stranded DNA, a one year shelf life at room temperature, and a very reasonable cost. The kit lists for $145 for the 250 prep size, which is the only size currently offered. Although this size might be overkill for some labs, the price and long shelf life make it somewhat easier to swallow.