We do a lot of DNA purification in the lab. Inevitably, we use kits produced by bioscience material manufacturers to do these purifications. Also, inevitably, we run out of the columns first.
Especially when realizing you’re buying the kits only to replace the columns, the costs of the kits can become even more jarring.
Here are some examples from our recent orders:
Minipreps – Zymo Research D4016 ZR Plasmid Miniprep-Classic – $736.35 for 800 preps or ~ $1/ sample (or column); this isn’t terrible!
Genomic DNA – Qiagen DNeasy – $946 for 250 preps or ~$4/ sample (or column); this is awful. Brian talked to the rep and got a discount to $3/ sample, but still!
Gel extraction – BioRad Freeze ‘N Squeeze – $244.59 for 100 preps or ~$2.5 / sample (or column). Also not great, considering we use a $1.5 / sample Zymo clean and concentrate kit afterwards, bringing the total to $4 / sample.
Thermo GeneJet Gel Extraction kit – $377.21 for 250 preps or ~$1.5 / sample (or column). [This was an Oct 2024 price]
Well, John is at the point of his PhD where he can go off the paved road and still get to where he needs to go. We had a short discussion that irt’s quite possible that many silica-based DNA binding columns were similar, and binding characteristics were more likely dependent on the buffers being used. He subsequently took it upon himself to try some off-brand columns in place of the Qiagen ones when using the DNeasy kit.
Bioland Scientific LLC Plasmid Miniprep Column – $102 for 250 preps or ~$0.4 / sample.
Omega Bio-Tek HIBIND DNA MINI COLUMNS 2 – $54.39 for 50 preps or ~$1 / sample.
When John took the same sample and processed them in triplicate, either using the included $4 Qiagen column, the $0.4 Bioland column, or the $1 Omega column, these were his results:
So everything yielded between 1 to 4 ug of genomic DNA (by Qubit / dsDNA binding dye), with Omega consistently in the low but usable range, and Bioland and Qiagen columns working better (and averaging almost 3 ug). We’ll still need to amplify and/or check the sizes of what was captured, but in terms of yield, they all seem to work.
But also, John didn’t stop there. We also do a fair amount of gel extractions. Some people use the Thermo dissolving kit, but John seems to prefer the Freeze-n-Squeeze and Zymo Clean-and-concentrate method. Here, he decided to use old unused filter tips to replace the BioRad FnS column. For the P200 filter tip, apparently all that was needed was snipping off the tip and sticking the remaining bit with the filter into a 1.5mL microcentrifuge tube. It was apparently much harder to get the P1000 to fit, but got something to work. Here are the results:
So they all work, and yielded between 250 and 400 ng of DNA, each. While the P1000 tip gets eliminated for impracticality, the tens of cents of P200 filter tips did as well if not better than the $1.5 columns made for this specific purpose. We also had a short discussion about what’s actually going on here, and apparently it’s a form of freeze drying (freeze and add pressure to extract liquid with DNA).
It’s still very preliminary in a sense (still need to repeat these experiments at some point), but I do think it’s a nice indication / reminder that we might not have to pay unnecessary amounts for kit-specific name-brand DNA binding columns.
Some other things to perhaps try:
RNA extraction – Qiagen RNeasy – $1,900 for 250 preps or ~$4 / sample (or column). Gotta try this next!