Re: [ccp4bb] usefulness of cacodylate?

[Boaz Shaanan]

Hi Frank, As the old saying goes: it's all relative (maybe not so old actually, it's only since Einstein's relativity theory, right?). Cacodylate was used, among other things, in buffers as a substitute for phosphate, merely because it kills bugs. Nowadays, we use azide, which is just as hazardous (well maybe not, if you read the details on the bottle) but still not recommended. And as Raji and others have pointed out, our heavy atom compounds, acrylamide, ethidium bromide, you name them, are not nice either. We have to take precautions of all sorts and I guess that's what your review committee will be looking for. I'd give them the credit that they're sensible people, unlike our University administration that declare ALL chemicals as dangerous (regardless of the data sheet), including NaCl, glucose, Superdex columns etc. whatever we order, just so that they can charge us 1.5% extra on the price (which is already much higher than what you pay) as we order the goods,  all under the pretext  that it's for disposing of the material out of the lab some time in the future (of course Superdex columns are never being disposed, and so is NaCl which is used to the last grain). Meanwhile, the admins can use the money for their needs.  Clever people, right?   Cheers,          Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Raji Edayathumangalam [r...@brandeis.edu] Sent: Friday, November 09, 2012 3:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] usefulness of cacodylate? Hi Frank, I worked with protein purification buffers and crystallization buffers containing 20mM potassium cacodylate for five years or so. And yes, the only precaution I used was gloves while weighing the chemical and while making buffers etc. And not just me, but all of my former colleagues worked with cacodylate. Then, there's those nasty chemicals for heavy atom soaks like mercury and tantalum compounds that are equally hazardous. And... many other chemicals we used on a daily basis in the lab but we don't suspect as much as we should. Nucleosome core particles stubbornly refuse to crystallize if you leave out cacodylate, not just from the crystallization buffers but also from the protein purification buffers. Yes, there are folks who accidentally left it out and never gotten crystals of nucleosomes. I don't rule out that someday someone may very well be able to substitute cacodylate for some other chemical and successfully crystallize nucleosomes.  It might be hard to interpret the kind of studies you suggest and here's why, in my opinion. Even if one showed that there was no need for cacodylate for, say, a 1000 different proteins, I would definitely not exclude it from a crystallization screen for my favorite protein because we have not gotten to that point in crystallography where one can predict crystallization conditions for a new macromolecule with great accuracy. In my opinion, it's all relative. There are probably more chances of me being killed by a reckless bicyclist in Boston/Cambridge than by cacodylate. ;-) Cheerios! Raji On Fri, Nov 9, 2012 at 7:26 AM, Frank von Delft <frank.vonde...@sgc.ox.ac.uk> wrote: Hi all - Anybody know     a) how hazardous is cacodylate?     b) does it really matter for crystallization screens? It seems by far the most hazardous component of the standard screens;  this 2011 paper seems to think so (bizarrely, I can't access it from Oxford): http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.1977.tb01136.x/abstract and this is site says lethal dose is 0.5-5g/kg: http://cameochemicals.noaa.gov/chemical/4468 meaning 2ml of a 0.1M solution contains 1/10th lethal dose...? (Someone should check my maths...)  [Coarse screens come mixed 2ml per condition.] Has anybody done careful experiments that showed it really mattered for a given crystal -- or even an entire screen? So I'm inclined to toss it out entirely rather than make crystallization screening a "hazardous activity".  (We're being subjected to a safety review.) Thoughts welcome. phx -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University