MadSci Network: Molecular Biology

Re: Why does DNA, NOT denature in phenol?

Date: Wed Feb 28 06:23:31 2007
Posted By: Sebastien De Landtsheer, Undergraduate, Immunology, Laboratoire National de Santé
Area of science: Molecular Biology
ID: 1169704599.Mb

Hello Matilda,

Your question is very interesting, thank you for being curious ;-)

When purifiying DNA, adding phenol to water will make the environment more hydrophobic. This is why this treatment denatures proteins, as the hydrophobic amino acids, that are "hidden" inside the proteic structure, will face outwards, increasing entropy...

But it is not the same for DNA, as the bases ARE NOT hydrophobic. Ok, they might be a bit less polar than a phosphate-ribose backbone, but they are still in the urge for hydogen bonds, and DNA remains a very hydrophilic compound... Thermodynamicly speaking, the two strands of DNA decrease their free energy by sticking to each other. Taking them apart would cost a lot of energy, which is not "re-funded" by the enrgy gained in solvatation. (one of) the only way to denature DNA is to decrease the dielectric constant of the medium, what you do by adding alcohol and salts. In this case, water is not available anymore for the DNA, and the only thing DNA can do, as a polar substance, is sticking to the ions, what is called precipitation...

I hope I answered your question


Sebastien De Landtsheer, Mad Scientist...

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