DIY Silicon dioxide DNA extraction matrix…from shoe desiccant?

Published: May 8th, 2016   Last Modified: November 17th, 2017

The grey-beards among you remember a time, when dinosaurs roamed the earth, before silicon dioxide based spin columns were commercially available. The times when you had to expose yourself to phenol/chloroform just to purify some DNA. I was trained in a similar manner, with your standard Sol’n 1-2-3 miniprep and PCI extraction. But once you have a little taste, just a taste, of the convenience, reproducibility and lack of phenol it can be hard to go back. Good spin kits (Macherey Nagel, mmm) can cost up to 2$ a prep and if you shop around you can get them for 0.50$ a prep without some of the frills, buffers or German engineering. I’ve heard of do it yourself silica matrix from various sources such as glass wool or diatomacieous earth but never really found a protocol that seemed easy and straightforward. Recently though I struck protocol gold, a method where you can make silicon dioxide DNA extraction matrix easily, cheaply and if you’re really desperate, from shoe desiccant.

First, credit where credits due, everything I’ve done here is based on a wonderful paper from the Jen Sheen lab. This paper goes over very thoroughly how to make SiO2 matrix for extracting DNA from solutions, like miniprep lysate, a PCR reaction, what have you. The paper gives you all the buffers you need to make it work, and essentially you are performing a home-brew version of a commercial spin kit inside a centrifuge tube. The only real costly reagent is the sodium iodide, which functions as the chaotropic agent that helps the DNA bind to the silica. Total cost though is cents, CENTS per prep.

The SiO2 matrix is made very simply. You buy SiO2 from Sigma, re-suspend it in water, discard the supernatent after two hours, re-suspend it again, discard the supernatent again after two hours and what’s left is your matrix! Nice and simple. Now, what if you’re jacked up on coffee, ITCHING to give it a go, but you realize Sigma isn’t exactly going to answer your calls on a weekend. What to do, what to do? Find another source for silicon dioxide.

Spice stores carry silicon dioxide powder sometimes (It’s in alot of processed foods, gah!), but nothing nearby. Glass wool? Not bad, but it’s likely soda lime glass which has other ingredients other than SiO2. What about dessicant packs? 100% SiO2 baby, yeah! FYI though, you can’t use dessicant packs with color indicator…it can be cobalt giving it color, yikes.

So, cut open the 5 gram dessicant pack, grind it up in a mortar and proceed as in the protocol. Couple of gotchas though. You will likely be unable to grind the SiO2 as fine as you can get it from Sigma, so after re-suspending your ground SiO2, discard the PELLET after 30 minutes, this is all large SiO2 particles and are no good for the experiment. Then proceed as normal, let settle for two hours, discard SN, etc.

Turns out, it worked! When compared against SiO2 ordered from Sigma, dessicant pack SiO2 works just as well. However, as much fun as McGyvering SiO2 from dessicant is, you should probably just be patient and get it cheaply from Sigma. Let me tell you, hitting little glass pebbles with a pestle can scatter them far and wide, and your supervisor may not appreciate having a bit of a crunch underfoot.