question about making phenol/TE and

[Zhiqun Li]

Thanks to you all for your inputs, they are very helpful! Ever since  
I posted my question to this email list, I got quite a few responses  
and I will follow those suggestions, like mixing the phenol with  
higher concentration of Tris-Cl at the first round followed by TE  
buffer equilibration. One friend also suggested me mix phenol and TE  
then stir the solution for overnight and let it sit like that  
afterwards. These all seem better ways than those I read from the  
protocols I have.

An issue regarding handling the toxic reagents / buffers in the lab:  
I agree that as a biologist, we sometimes indeed have to know how to  
handle these materials carefully. However, there are pre-made  
buffers / solutions and if we simply buy them, we will save time, as  
well as saving us from dying at an early age. We do prepare a lot of  
toxic solutions by ourselves in our lab, and I never really thought  
about the problem that can bring to us until this time the phenol did  
make my throat feel gross for a whole day (just simply by inhaling it  
- even I was handling it in a chemical hood and didn't get any single  
drop of phenol spilled on to myself). I've thought about this, and  
discussed with some of my colleagues, I think we will bring up a plan  
to our advisor for suggesting what kind of buffers we should make by  
ourselves, and what kind of solutions (like phenol/TE, phenol/water  
and EtBr etc) we should buy. Imagine that, we cannot even get a mask  
for working with these reagents, this is really a serious issue we  
need to work on.

L

On Sep 17, 2006, at 10:45 PM, DK wrote:

> In article <everg2d25cg47cllj7pii7kdgfsked5q51 at 4ax.com>, ChenHA  
> <hzhen at freeuk.com> wrote:
>> On Sun, 17 Sep 2006 18:46:10 GMT, dk at no.email.thankstospam.net (DK)
>> wrote:
>>
>>>
>>> What's the big deal? Any lab is full of stuff that's 100X more toxic
>>> than phenol.
>>
>> I heard from  someone that if you stick your hand into phenol, the
>> amount absorb through the skin would be enough to kill you.  It might
>> be one of those myths that go round in the lab, but it does make you
>> cautious when handling phenol.
>
> Nearly every lip balm contains 0.5-1% phenol (w/w). I was insanely
> scared one day when we discovered that out tiny god managed to steal
> and eat the whole 5 g of the lip balm. The vet assured it will be fine
> and it was. No problem of ingesting 50 mg phenol per 5 kg of body
> weight. For a human, it would correspond to minimum of 0.5 g - the
> amount that normally gives heart attack to people afraid of phenol.
>
> I am not saying phenol is safe - just like with EthBr, one has of  
> course
> exercise caution but it's still good to remain rational, particularly
> when one calls oneself a scientist.
>
>> However, I have use TCP (an anticeptic liquid) which contains a  
>> bit of
>> phenol in the past for wounds as well as gargling.  Victorian ladies
>> also use diluted phenol (they called it carbolic acid) to whiten  
>> their
>> skin.   I have noticed that my fingers turned ghostly white when
>> little bit of phenol get onto the skin.
>
> Little wonder - it's a very strong protein denaturant. Phenolic skin
> peeling is a risky but effective cosmetic procedure...
>
>>> If a person can't handle phenol and the likes properly,
>>> that person should stay away from the lab for the reason of being a
>>> danger to oneself and everyone else around.
>>>
>>> To the original poster: I recall that either the buffer has to be  
>>> quite
>>> concentrated during first extraction(s) (100 mM Tris instead of
>>> 10 mM) or the equilibration has to be done many times. It is also
>>> possible that your phenol is old and oxidized. It is oxidized by  
>>> O2 quite
>>> readily - that's why hydroxyquinoline is added to it for solution  
>>> used in
>>> molecular biology. Old phenol usually turns pinkish and in my
>>> experience takes longer to neutralize.
>>
>> If it is pinkish, you shouldn't use it at all, no?  Pink phenol is a
>> sign of oxidation and can damage the DNA.
>
> I am totally not sure but I thought that main oxidation products are
> quinones and their polymers and that they are "DNA neutral".
> Long time ago when I did use pink phenol, I had no other choice
> anyway. Everything worked, no complaints.
>
>> I'm also one of those who would rather buy ready made equilibrated
>> phenol rather making it myself.   Too much trouble methink making it
>> (I think it needs distilling doesn't it when you start with solid
>> phenol?).
>>
>> I've seen people working in rich labs who would buy almost everything
>> ready made (not just things that take a bit of time to prepare like
>> gels, but also water, Tris buffer, ready-cut aluminium foil for  
>> flask,
>> media, etc.).  Makes me somewhat jealous that they can afford to do
>> this, but I also think that it is bad practice because I'm not  
>> sure if
>> they even know how to do the very basic things that we take for
>> granted.
>
> That's the whole thing. When you have no idea how it's done and how
> it works, you can't troubleshoot and it's easier to screw up and never
> notice it. I am as skeptical of biochemists who can't pour and run
> decent-looking gel as I would be of a car mechanic who can't do the
> job without power tools and computer.
>
> DK
>
>
>
>
>
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