Cotton Wool Gel Purification
Full credit to Yuan Sun, Kannappan Sriramajayam, Dianzhong Luo, and D. Joshua Liao for this excellent and cheap protocol.
Original Publication: A Quick, Cost-Free Method of Purification of DNA Fragments from Agarose Gel
Equipment & Consumables:
22G Syringe Needle
Absorbent cotton wool (or) Glass Wool
500-µl Microcentrifuge tube (this specific tube size nests perfectly in an eppendorf)
Gel Slice containing desired band cut from an Agarose Electrophoresis gel
Protocol:
Use the syringe needle to poke a hole right in the bottom of the the 500-µl centrifuge tube.
Take extreme care not to poke holes in yourself
Tear off a small piece of cotton/glass wool and push it into the bottom of the tube (using the needle/alternative sterile tool).
Squeeze your gel slice into the 500-µl tube so that it is sitting on top of the cotton wool plug. Cap the tube and place it inside a sterile 1.7 ml (Eppendorf) microcentrifuge tube.
Spin at 5000-10,000 rpm for 5-10 minutes depending on the length of the DNA fragment.
<1 kb = 5,000 rpm, 5 min
1-2 kb = 10,000 rpm, 5 min
2-3 kb = 10,000 rpm, 10 minutes
>3kb = ?
Comments:
The authors of the protocol record a 30-60% recovery rate, with a theoretical maximum around 80%.
My biggest challenge with this protocol was reducing the elution volume at the end step. There is a surprising amount of liquid in a gel slice and you may find your recovery to be quite successful - but overly dilute. You may want to perform some kind of dehydration, via evaporation or vacuum manifold.
If I find a way to do this, this is a reminder to include that protocol.
