pink phenol - (Nov/14/2005 )
My phenol/chloroform stock is turning pinkish.
I understand this is a sign of oxidation of phenol and I should not use this stock, but could anyone tell me SPECIFIC reasons why you should not use pink phenol? Does it degrade DNA? Does it not extract proteins? Does it lose DNA in the organic phase?
(Also, everytime I use phenol, I dream of pink elephants that night. Could anyone tell me what this means?)
Pink elephants!!!
I think you probably worry too much about phenol turning pink!!
Get some new phenol.
Because oxidized phenol is no longer phenol, just like oxidized iron is no longer iron -- it is rust.
if phenol/chloroform gets pinK,it indicates that phenol has been oxidized to a mixture including catechol , hydroquinone and tars.
OK, so phenol gets oxidized, turns into something else. Fine. But I suppose it is a gradual process. Do you think even a small amount of catechol, hydroquinone, tars etc in the solution completely abolishes phenol's ability to extract proteins from DNA solution?
After all, a rusted car still runs and a rusted knife still cuts a tomato, unless they become 100% rust.
No. But when there's enough there to change the color of the solution, there's enough there to change the pH, which is the principal determinant of whether the DNA seperates into the aqueous phase or the organic phase.
Why would you bother trying to use this stuff?
I have just used some really pink phenol to isolate some tail DNA last week and got my DNA... I was not aware that pink means degraded. I haven't checked the 280/260, but directly digested and transfered to membrane and it worked OK. So.... you may be lucky sometimes (like I was) but try to stick to the rules. Otherways you'll have explaining to do to your PI.
Why would you bother trying to use this stuff?
Now that's the kind of answer I was looking for. Thank you.
Why am I so obsessed with the pink phenol? It's a long story...