Some protocols call for fluid samples to be mixed with a "vortexer" on the high setting. What effect does the vortexing have on fluid samples that mechanical shaking does not? Does it shear long molecules like DNA, for instance?

A friend is setting up a new lab and asked if vortexers were strictly necessary. I am aware they are often called for in various protocols, but I actually don't know what specific effect the vortexing has that makes it better than manual shaking. What do you think?

A typical lab vortexer


In my experience, shaking and mixing have different "dead spaces". Supposed you had an eppendorf tube and you stirred it around with a pipet tip for thirty minutes. You would have great convective mixing in the radial direction but virtually no mixing in the Z-direction. Supposed you had a very viscous fluid like PEG. If you set the tube on a shaker for an hour it will virtually not mix. The vortexer provides a very different profile of mixing.

Instances where I wouldn't use the vortexer would be for sensitive objects like DNA and cells.

(update) We had some interesting suggestions from the FDA (since the FDA pays attention to these type of discussions). To get proper mixing, it is often not considered enough to merely swirl a tube a bunch. Their actual recommendation is to train technicians to perform a 90 degree angle arc with their forearm to generate proper force in mixing.

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    $\begingroup$ A single vortex is essential for any "wet-lab" for the reason bobthejoe describes. The vortex not only provides a different profile of mixing, but has the power to mix viscous fluids that would otherwise remain virtually unmixed (glycerol stocks come to mind). Vortex shakers are contra-indicated for some lab protocols (like in miniprep kits) but can be used for most mixing needs. As an aside, vortexing of DNA is safe in my experience. Genomic DNA tends to shear if precipitated and then vortexed, but plasmid DNA and oligos are fine. $\endgroup$ – user560 Mar 16 '12 at 1:37
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    $\begingroup$ Vortexing is called for when one or more of the fluid samples is more viscous than water? For instance (as you suggest), 100% glycerol is 1000x more dynamically viscous than water, hence the need for a vortexer to mix water and glycerol well (wolframalpha.com/input/…). $\endgroup$ – Mac Cowell Mar 16 '12 at 3:25
  • $\begingroup$ Besides mixing fluids of different viscosities, are vortexers necessary for any other lab operations? $\endgroup$ – Mac Cowell Mar 16 '12 at 3:26
  • $\begingroup$ @Maccowell, doesn't mixing liquids of different viscosities describe most lab operation? I would also include suspending non-soluble mixtures. $\endgroup$ – bobthejoe Mar 16 '12 at 4:51

what specific effect the vortexing has that makes it better than manual shaking

In addition to @bobthejoe's answer about viscous fluids, (manual) mechanical shaking is also less consistent and more tiresome than vortexing.

If the vortexer is always at the same speed and each sample is vortexed for the same amount of time, then the shaking step will be less variable among samples. For example, the vigor of mixing an aqueous soil suspension could potentially affect the amount of aggregate decomposition and release of molecules into the suspension (I don't have a reference for this, but it is good practice to treat replicates the same to minimize any non-treatment effect).

Manual shaking is not only less consistent, it is also tiresome - especially with larger volumes (>=10ml) and large sample sizes.

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