MadSci Network: Biochemistry

Re: why is DNA denatured in sodium hydroxide solution(PH=12)?

Date: Wed Jan 5 22:12:35 2005
Posted By: Ara Kooser, Grad student, Physical Chemistry, Sandia National Labs
Area of science: Biochemistry
ID: 1098641676.Bc

The two strands that make up DNA are only held together by hydrogen bonding.

A good overview on hydrogen bonding is here 161Ahydrogenbond.html

The hydrogen bonding network can be very fragile. Heat, acid, bases can all disrupt this and cause the DNA strands to separate.

As you might know if you have played with DNA in lab NaOH is actually used to extract DNA from cells.

The best way to understand what is happening at the atomic level is to download a PDB file of DNA and look at it in a viewer (Hope this is of some use, I am slightly biased towards computational stuff ;) ).

You can download a PDB file from here ( pdb23_1.html), and some viewers are listed as well. I used the 108D.pdb file.

In terms of viewers, I prefer VMD (http:// because you can turn on hydrogen bonding. But with any viewer you should be able to see where the hydrogen bonds are. If you are feeling really inquisitive you can solvate the DNA and add Na OH to the system and run molecular dynamics on the system.

Journal Articles:

Charles A. Zittle. Enzymatic hydrolysis of deoxyribonucleic acid prepared with the use of strong sodium hydroxide. Journal of the Franklin Institute, Volume 245, Issue 1, January 1948, Pages 78-80.

John S. Ullman and Brian J. McCarthy. Alkali deamination of cytosine residues in DNA. Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, Volume 294, Issue 3, 4 February 1973, Pages 396-404

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