Hi!
I noticed that mostly the single cell assay use AMPure beads (magnetic) instead of purifying column.
But both function through a DNA affinity coating, just on surface in beads and on membrane in column.
Why not just use the DNA purifying column, which is far easier to manipulate?
Thanks!
Sure, you can just use column. However, I don't see a possibility of using columns if you have a full plate of samples. I don't understand your logic for deciding column are easier to manage.
We have used both in our lab, and I prefer the beads. There is always some loss of sample when doing a cleanup, and I feel that I get a better recovery of the target DNA when using a magnetic cleanup method (although it's been awhile since I've done a side by side comparison). With a column cleanup, if any liquid gets on the side of the tube, it can slide past the matrix and result in re-contaminating the sample that DID go through the column matrix. Even if you're carful with pipetting, sometimes static will pull a droplet of sample to the side of the tube. We use a lot of magnetic beads in our lab, and they consistently give the best results for us. Instead of AMPure, we've switched to a more affordable option, a drop-in replacement for AMPure, MagBio HighPrep PCR beads - and I love our sales rep.
On top of what others have said, columns have a finite that can be bound before you elute and have to add more to the columns. Magnetic beads on the otherhand can be done all at one since you can just add more beads (as long as your tube/well allows) and altering your bead ratio can allow for size selection too
Magnetic bead technology often functions by affinity interactions between ligands that coat the beads and their specific targets. We add magnetic beads to sample lysate; they bind to the nucleic acids in the sample, allowing easy removal of the non-bound molecules and contaminants. Contrastingly columns are composed of a compound such as silica that, in the presence of the right buffers, keeps nucleic acids bound to the column while other molecules are washed through. Magnetic beads are stable with a high binding capacity and larger surface area and show adaptability with samples of different viscosities.
Magnetic beads are perfect for high throughput applications, they can be automated on KingFisher Flex or similar instruments and enable handling 100's of samples per day. Spin columns are perfect for lower throughput, typically when you process less than 24 samples at a time
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