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Let's suppose the concentration of a 20-nt DNA strand is $10^{-4}$M and the solution does not contain any salt ions. In a solution with pH 7, $[H^+]=10^{-7}$M, on average each DNA has only 0.001 protons. But the DNA phosphate groups become charged through de-protonation so each DNA should effectively release 20 protons thus we would expect $[H^+]=20\times 10^{-4}$M. How does the system maintain chemical equilibrium while keeping charge neutrality? If $[H^+]=10^{-7}$M because pH=7, where do other protons go?

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    $\begingroup$ If you added DNA with a protonated phosphate backbone to a sample of pure water with pH of exactly 7.0, the extra protons on the backbone would be picked up by waters to create a deprotonated backbone and hydronium ion. The charge is still balanced, the backbone becomes negative and the hydronium is positive. The pH would change, becoming more acidic, I don't know how acidic, depends on the amount of DNA and equilibrium constants, and I don't want to do that math right now. $\endgroup$ – user137 Apr 13 '15 at 15:56
  • $\begingroup$ I'd suggest specifying in your question that your system is just water at some sort of default conditions. $\endgroup$ – aaaaaa Apr 13 '15 at 16:52
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DNA stands for deoxyribonucleic acid. Acid, by definition and mechanism in aqueous environment, is something that donates proton ($H^+$). HCl dissolved in water will donate proton to solution, thus bringing pH down, since $pH=-log_{10}[H^+]$.

DNA, being an acid, donates protons to water and brings pH down a notch. Just like in case with HCl, it has nothing to do with keeping charge neutrality. Water is not a buffer, that is able to tolerate or smooth change in pH. What happens when you add DNA to buffered solution, say phosphate buffer, is completely different story from biochemistry.

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    $\begingroup$ Note that DNA also has "bases".. But since they are paired, they may not contribute to basicity. $\endgroup$ – WYSIWYG Apr 14 '15 at 4:30
  • $\begingroup$ indeed. Single-stranded DNA will act differently $\endgroup$ – aaaaaa Apr 14 '15 at 5:07
  • $\begingroup$ The nitrogenous bases are Lewis bases (that can donate an electron pair) and are extremely weak, similar to pyridine. $\endgroup$ – mdperry Apr 15 '15 at 2:28
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Since DNA is an acid it is reasonable to ask: what is the pKa of the phosphate residues located all along the polynucleotide's sugar-phosphate backbone? Apparently that number is at a pH between 1 and 2 (http://www.bio.brandeis.edu/classes/biochem104/DNA_lecture.pdf). That means at physiological pH ranges (for example, the pH found inside the nucleus or cytoplasm of a cell, around 7 or so) 100 % of these phosphates would be ionized (unprotonated), and therefore strongly negatively charged. The counter ions would be any suitable mono- or divalent cations handy. When you purchase intact DNA the fibres are typically the sodium salt--I believe this is similar to the material Wilkins & Franklin used to obtain the images Watson & Crick used to solve the structure.

So strictly speaking, the experimental situation described in the question does not exist. You could never obtain a pure sample of protonated DNA that you could then add to pure water. At the pH the DNA would be protonated the DNA would depurinate leading to strand scission at the abasic sites. This is the whole principle of soaking your agarose gel in HCl in preparation for a Southern Blot, to fragment the high molecular weight fragments so they will migrate more efficiently out of the gel and onto the blotting membrane.

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    $\begingroup$ nice expansion of original problem! $\endgroup$ – aaaaaa Apr 15 '15 at 3:54

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