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I understand how DNA precipitation works in the presence of salt (such as 0.3 M sodium acetate or 0.2 M sodium chloride) and alcohol (30 ~ 50 % isopropanol or 60 ~ 75% ethanol)

However, in the Trizol kit manual, DNA could be washed and precipitated in 0.1 M sodium citrate in 10% ethanol

At only 10% ethanol and 0.1 M sodium ion, how can DNA be in a "compact/insoluble" form so it can be precipitated by a low speed centrifugation (2000 x g for 5 mins)?

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The sodium ions will bind to and neutralize the (-) charge on the phospho backbone of DNA. This reduces hydrogen bonding sites for water, which then results in less solubility.

Edited for clarity and because I didn't answer the question the first time. Sorry about that.

The extraction of DNA is from the interphase layer, which is a very small fraction of the original sample. The extraction of the interphase layer is then mixed with 100% EtOH (300 ul per 1.0 Trizol used in that sample). This should actually be 60% or more EtOH based on my experience using this method.

That is the precipitation step.

The fact that the wash has only 10% EtOH and 0.1M sodium citrate and that is still sufficient to keep DNA precipitated revolves around 0.1M sodium citrate is usually 0.3M sodium ions (sodium citrate can be mono-, di- or tri-sodium, but unless specified..sodium citrate implies tri-). Remember for the wash, you don't need to do a quick precipitation, you just need to prevent it from solubilizing again.

I am removing my comments that contained the same information.

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  • $\begingroup$ This doesn't address why only 0.1 M sodium citrate and 10% EtOH is used while most precipitation protocols require 0.3 M sodium acetate in 70% EtOH $\endgroup$ – Green Jan 24 '16 at 23:34

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