I'm trying to figure out what kind of effect adding too much sodium acetate during an SDS DNA extraction.

I know the sodium acetate is used to neutralize the negative charge on the PO3 in the DNA backbone, bringing it out of solution.

My question is would too much sodium acetate have an adverse effect strictly due to the change in pH? That is, break down the DNA backbone because of the significant change in pH of the solution, therefore destroying the product? If not, then what other effects can this have?

Thanks.

I'm not sure, but my gut feeling is no. The acetate buffer I use is at pH 4.8, which I don't think is low enough to cause any actual damage to the DNA, on purely pH grounds. Having said that, at sufficient concetration the acetate might start doing nasty things directly to the DNA by electrophilic attack. Any chemists out there able to expand on that?

It will have little effect - you can just re-precipitate the DNA and re-suspend in TE to bring the pH back to normal

Muhammad,

What exactly is the problem you are having with your chromosomal DNA prep? Are you encountering a lot of sheared DNA? Are you working in a school lab class using a crude chromosomal prep protocol, or an equipped laboratory on a research project?

Sodium acetate shouldn't pose an issue, even at the often used pHs of 4.8 - 5.2 and at up to 0.5 M. If you are using much higher concentrations than this (and I'd ask 'Why?' if you are), then the only issue you would routinely encounter is that your DNA pellet will be very salty, and take a great deal of washing to de-salt.

If you are encountering excessive shearing, you might look to your earlier handling of your DNA, mixing less vigorously, and ensuring that you have taken appropriate action for nucleases that can degrade your DNA - which of course will depend on what materials you have access to.