Do we need the bioruptor?

[SeqGeorge's]

We’ve recently bought an Ion Torrent and have just received our training.

Whilst setting up the lab we purchased a Bioruptor as we thought it was an essential piece of kit – but it seems that the new enzymatic fragmentations may mean that we don’t need the Bioruptor. As it’s still sat in its box, unpackaged, we’re considering whether we should return it or sell it on, unopened.

Does anyone have any experience comparing results of enzymatic and mechanical fragmentation?

[bioits]

I guess it really depends on your application. Enzymatic method will always has more or less bias comparing to sonication one. If the little bias doesn't bother you, sell or return the bioruptor.

[epistatic]

Enzymatic: works well for non-degraded, clean, high molecular weight DNA. If DNA is degraded or dirty, the fragmentation time is less consistent. It is harder to go back and shear just a bit longer if the fragments are not in the range you need.

Bioruptor: More consistent, can alter the shearing protocol easily depending on DNA quality. Easy to take an aliquot of the sheared material, QC, and run the sample longer if needed.

I like enzymatic shearing in theory, but in practice find it more problematic when I get a lot of DNA samples with varying degrees of concentration and quality.

[T199Y]

Hi,
Can I ask how much you paid for the Bioruptor?
Thanks.

[ETHANol]

Agree with epistatic enzymatic shearing in theory works great. If you are processing the same type of sample then you can easily standardize. But if there is variation between your samples that will be magnified with enzymatic shearing. Of course with acoustic shearing you will see differences between samples but the variation is not as great.

I wouldn't send it back. It's a small price compared to what you will spend on everything and it is a nice tool to have in your toolbox. But it really depends on what you are going to be doing.

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Ethan

[SeqGeorge's]

Thanks for all your replies.

The consensus seems to be to hang on to the Bioruptor. Although the PGM is intended for small labs, we anticipate working with a range of people from across the university (and hopefully beyond). This means the samples we'll work with (and their quality) will change between projects. Given this, your comments seem to suggest that the Bioruptor will more easily allow us to generate optimally fragmented DNA than the enzymatic protocol.

T199Y: I don't have the info to hand about how much we paid for it. Were you hoping to make us an offer on it?

SG