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Isopropanol, Water, and RNA Stability

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Isopropanol, Water, and RNA Stability

Postby cw11 » Mon Nov 28, 2011 7:15 pm

I was recently having a discussion with someone who remarked in passing that RNA stability is higher in isopropanol than in H2O. (I am preparing to perform a phenol:chloroform extraction of RNA, and they recommended - for added stability - that I keep the RNA in isopropanol instead of H2O until I'm ready to use it).

What is the chemical/biological basis for the increased stability of RNA in isopropanol? I assume it has to do with the higher polarity of isopropanol relative to water?
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Re: Isopropanol, Water, and RNA Stability

Postby JackBean » Mon Nov 28, 2011 9:41 pm

isopropanol is more polar than water? :roll: You should probably recapitulate some general chemistry.

here is the mechanism:
Image
thus you can see that OH- is important for the hydrolysis
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Isopropanol, Water, and RNA Stability

Postby cw11 » Tue Nov 29, 2011 1:44 am

Ahhh fail! Thanks for your reply!

But in that case, it doesn't really actually have to do with the polarity, does it? It has to do with the pKA of the substances involved. Isopropanol, as an alcohol, has a pKa of around 16; water has a pKa of 15.7. So water is very slightly more likely to become OH- than isopropanol is to become RO-, leading to the higher relative stability of RNA in water. Y/N? (My sad attempt to dredge up old OChem memories...)
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Postby JackBean » Tue Nov 29, 2011 6:49 am

I found value 17 http://chemweb.unp.ac.za/chemistry/Phys ... values.htm
However, the value is of isopropanol in water, where the H+ is accepted by H2O, the situation in 100% isopropanol will be little bit different.
Also, even if the anion occured, the molecul is quite huge and the access to RNA molecule is harder.
http://www.biolib.cz/en/main/

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