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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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In the Pipeline

« The Scent of Food Is Enough? | Main | Chemistry In (Ahem) Everyday Life »

April 29, 2010

Curse of the Plastic Tubes

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Posted by Derek

In keeping with the problem discussed here ("sticky containers"), there's a report that a lot of common spectrometric DNA assays may have been affected by leaching of various absorbing contaminants from plastic labware. If the published work is shown relative to control tubes, things should be (roughly) OK, but if not, well. . .who knows? Especially if the experiments were done using the less expensive tubes, which seem to be more prone to emitting gunk.

We take containers for granted in most lab situations, but we really shouldn't. Everything - all the plastics, all the types of glass, all the metals - is capable of causing trouble under some conditions. And it tends to sneak up on us when it happens. (Of course, there are more, well, noticeable problems with plastics in the organic chemistry lab, but that's another story. Watch out for the flying cork rings!)

Comments (12) + TrackBacks (0) | Category: Biological News | Life in the Drug Labs


COMMENTS

1. Betsy on April 29, 2010 12:17 PM writes...

I'm in an Assay & Screening group, and plastics are the bane of our existence. For some reason, vendors keep "improving" their assay plates by mucking with the plastics, and it often throws our biochemical assays completely out of whack. I shudder to think about how much time we've wasted reconfiguring assays to work with the "new" plastics. GRR!

Permalink to Comment

2. J-bone on April 29, 2010 12:49 PM writes...

Ha ha! I enjoyed that archive blog entry tremendously. I've had similar freakouts, but I won't go into detail. Main idea: my advisor walked into the lab just as I spilled quite a bit of product and began to pepper the surrounding area with some choice words.

Permalink to Comment

3. p on April 29, 2010 12:53 PM writes...

I know new students have hit bottom when they bring me their NMR of some phthalate, unable to figure out what it might be. From there they usually improve rapidly.

Permalink to Comment

4. Hap on April 29, 2010 12:55 PM writes...

The archive post sounds about right, though I wonder if I could have controlled myself that much. I think a solvent jug might have died that night (sans solvent).

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5. lynn on April 29, 2010 1:35 PM writes...

@Betsy
Paper or plastic?

Back in the day I spent 3 months dealing with changes in Whatman DE81 filter paper necessary for an assay critical for my post doctoral work. Different batches required different washing regimens in order to retain ribo-oligonucleotides but not rNTPs. Hmmm, an HPLC might have helped, eh? Or maybe there's a kit for that now...

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6. Handles on April 29, 2010 6:16 PM writes...

@p
Others are unlucky with their advisors, and the embarassing phthalate work is published:

http://www.ncbi.nlm.nih.gov/pubmed/18826136

Permalink to Comment

7. Dana on April 30, 2010 7:27 AM writes...

Cheap and/or colored microcentrifuge tubes are the bane of electrospray mass spectrometry. The cheap ones from the stockroom leach like crazy and the dyes in the colored ones are even worse. We've found that Eppendorf brand tubes work the best. In LCMS it seems to be less of an issue, but when you just have one sample in a tube it can be a huge problem.

Permalink to Comment

8. tj on April 30, 2010 8:32 AM writes...

In the past we have had problems when using plastic kit for small libraries, with the sharp almost-singlet signals around 1ppm in the proton NMR requiring a further purification before registering the compounds. Out of curiosity, does anyone know what this stuff is? Apparently the usual phthalates aren't involved as there are no aromatic signals.

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9. p on April 30, 2010 8:36 AM writes...

Handles, that's awesome. What a find!

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10. qetzal on April 30, 2010 4:05 PM writes...

Ditto Dana on the Eppendorf brand tubes. I occasionally have reason to do depurination studies that involve heating oligos in dilute HCl. Most tubes leach a ton of UV-absorbing material under those conditions, but the Eppendorf tubes (cat. #022363212) do not.

Checking my notes, incubating the Epp. tubes with 0.1 N HCl at 70C for 2h, the mean A260 was -0.003 +/- 0.001 (mean +/- sd; blanked vs. unheated stock 0.1N HCl). 6 other brands & cat. numbers of tubes gave mean A260s ranging from 0.030 to 0.400!

Of course, everyone's needs will be different, & there's no guarantee that Epp. brand tubes will work for you. Or that Epp. won't suddenly change their manufacturing & screw you up without warning. Still, I'd probably start with them if you need low-leaching tubes.

Discloosure: I have no interest in Eppendorf whatsoever. Just hoping to help others avoid some of the pitfalls I've stumbled into.

Permalink to Comment

11. Sili on May 1, 2010 3:28 PM writes...

The old PI next door told of how one of his students had great trouble getting NMR clean samples off prep TLC.

A while later the syntheses were redone, but the new student made sure to use cork stoppers instead of parafilm. Result: lovely crystals.

Permalink to Comment

12. Sili on May 1, 2010 3:31 PM writes...

Oh, and in re that old post: Write that damn book.

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