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I have a question about the role of NaCl in the DNA extraction process. So for NaCl concentrations under 0.5M, CTAB and DNA molecules can create complexes. In those concentrations, proteins and other hydrocarbons are still soluble in water except the DNA-CTAB complex. If we raise the concentration of NaCl then the complex of CTAB-DNA will be soluble to water too. Correct me if I'm wrong until now.

So I don't understand something. Why do we use NaCl?

Let's assume that we don't add NaCl. Will the CTAB create complex with DNA or not? As I read CTAB creates ionic bonds with DNA (phosphate groups). So in this situation (without NaCl) CTAB must be able to create complex with DNA too.

So why did we use NaCl? Just to keep proteins and other hydrocarbons soluble in the water or there is something else that NaCl helps in this complex creation?

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NaCl provides Na+ ions that will block negative charge from phosphates on DNA. Negatively charged phosphates on DNA cause molecules to repel each other. The Na+ ions will form an ionic bond with the negatively charged phosphates on the DNA, neutralizing the negative charges and allowing the DNA molecules to come together –  Ahmad Dec 8 at 21:31

2 Answers 2

up vote 3 down vote accepted

CTAB forms insoluble complexes with nucleic acids and can be used to selectively precipitate them from solutions, see this reference:

When you add NaCl in a concentration between 0.4 - 0.7M, the nucleic acids stay in solution, while polysaccharides and other substances, which may interfere with the DNA preparation do not. See this paper: "Rapid isolation of high molecular weight plant DNA."

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DNA molecules are negatively charged so they repel one-another, which makes it difficult as it is to pellet. Hence Na+ ion from NaCl binds with the negatively charged DNA and neutralises the overall charge. Thus Na+ prevents the repelling of DNA molecules.

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This explanation is wrong. CTAB is positively charged, binds to the DNA and precipitates it. A higher ionic strength of the solution (above 0.5 M NaCl for example) will disturb this interaction and bring the nucleic acids back into solution. –  Chris Dec 9 at 20:35

protected by Chris Dec 8 at 21:54

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