A penny for your method: PCR cleanup

Very rarely, in scientific research, do we get the opportunity to do less with more. As a result, one thing that we are good at is stretching a dollar. To (hopefully) contribute something back to the struggle, I’ve decided to start an intermittent set of posts that focus on reducing the cost of common laboratory methods.

Sometimes, I’ll present protocols or links to protocol, and others I will likely lay out many of the essentials, and let you fill in the blanks. Occasionally, my suggestions will be pretty simple – but saving money is saving money, right?

As part of this effort, please send the real golden-nugget, dollar-saving lab hacks my way (molecularecologist+pennymethod@gmail.com), and I’ll do my best to curate what I get and post the golden-est of nuggets I receive right here (with attribution, of course).

Now, with that out of the way, I’ll start the party with PCR cleanup – specifically medium-throughput cleanup (i.e., 96- or 384-well).

The gist of PCR cleanup is that you often want to remove unincorporated primers, left-over dNTPs, salts, and other “stuff” from amplicons before you do other things with them. Kits are a handy solution to the cleanup “problem” because they’re pretty fast, extremely convenient, and largely idiot-proof. Commercial options for these sorts of kits include those from Qiagen and Zymo, among others. The Qiagen QIAQuick™ kits (p/n 28181) list at $670.00 per kit (4×96-well plates) or $1.75/sample. The Zymo ZR96 DNA Clean & Concentrator™ (p/n D4023) kits (2×96-well plates) list at $189.00 per kit or $0.98/sample.

But, all of these are too rich for my blood. I could probably do EtOH precipitation in 96-well plates, if I were really hard-core, but I’m not always really hard core nor do I like to spin plates eternally, if i can help it. And, 96-well EtOH precips in inexperienced hands can go horribly wrong. Bottom line is that there’s a better solution available – easy and idiot-proof like the commercial kits and inexpensive like EtOH precipitation:

Cost for this operation is $0.25/sample for the DNA Filter plate, $0.05/sample for the flow-through plate, and $0.04/sample for the DNA storage plate – for a grand total of $0.34/sample (chemical cost is largely negligible on a per sample basis, but add $0.01/sample, if you like). This represents a savings of 65% over the Zymo kits and 80% over the Qiagen kits. You can reduce costs further by re-using the flow-through plates – treat them in 10% bleach if you are concerned about cross-contamination.



About Brant Faircloth

I'm an Assistant Researcher at the University of California - Los Angeles. My interests include mating behavior, social behavior, the (immuno-)genetic basis of mate choice, genomics of non-model organisms, metagenomics, computer programming, and the integration of molecular and field biology.
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