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DNA solubility data in only water is scarce.

A previous question asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple since no data seems to exist for DNA solubility in exclusively water.

Even the small amount of data about water was in the context of washing away organic compounds from the solution. This got me thinking. DNA is in an aqueous solution in biological situations, and is usually handled in aqueous solutions in labs. So why is solubility data so scarce for pure water? What is important about organic compounds for DNA solutions?

Why are other additives important for laboratory DNA solutions?

So my question is why is DNA dissolved in exclusively water seemingly "uncommon" in laboratories? Is there something about pure water that is bad for DNA storage? Is it that functionally DNA never needs to be in water because it is inaccessible to proteins? Or have I misinterpreted the lack of solubility data; water is common-place and no data exists because there is no need?

I imagine PCR is where most of the data on DNA solutions exists. What about the polar organic solvents/compounds makes them important for DNA solutions?

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James
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    I routinely dissolve minipreps and maxipreps in water or Tris buffer. It is most certainly not irrelevant in laboratories. PCR can't use water as the buffers are necessary for the activity of the polymerase. – March Ho Jun 28 '15 at 17:53
  • @MarchHo Thanks for the insight. I think the idea of buffers probably also goes beyond PCR. I didn't intend to dismiss water as irrelevant - I just wanted to highlight there is little/no research that has been done on water as a solvent by itself. – James Jun 28 '15 at 18:15
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    Double-stranded DNA, with its strongly polar sugar-phosphate backbone, is negligibly soluble in non-polar organic solvents. Could you please provide a link or cite a reference where they dissolved any nucleic acids in non-polar solvents? – mdperry Jun 28 '15 at 18:25
  • @GoodGravy DNA is evolved to function in aqueous environment. Perhaps it may dissolve in other polar non-aqueous solvents but I don't think non-polar solvents can dissolve it. As you might already know, even polar non-aqueous molecules like ethanol precipitate DNA (It precipitates with acetone too- I tried it a few times as a fun experiment). Which solvents are you talking about? – WYSIWYG Jun 28 '15 at 18:49
  • Thanks for pointing out the "non-polar" mistake. I meant polar: ethanol for example. – James Jun 28 '15 at 18:54
  • @GoodGravy But DNA is never dissolved in any non-aqueous solvent. DMSO and formamide are used in PCR but not as solvents. – WYSIWYG Jun 28 '15 at 19:24
  • @WYSIWYG Ah I see your point. Your point also re-enforces why it's so weird to me; no pure water solubility data seems to exist despite DNA being dissolved almost exclusively in aqueous solutions. Some other compound is always present. I cannot believe that there has never been a control done on DNA solubility in pure water. – James Jun 28 '15 at 19:49
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    http://www3.idtdna.com/pages/support/technical-vault/faq-old/application-support/storage/faqs/2011/07/01/what-is-the-maximum-solubility-of-dna-in-water-(weight-unit-volume-unit)- How about this. – 243 Jun 28 '15 at 21:35
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    DNA dissolves perfectly in plain water - there are no other additions needed. The reason you use Tris-EDTA buffer is that is better for storage. About what other organic compounds are you thinking? – Chris Jun 28 '15 at 21:57
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    The only organic solvents I have used with DNA/RNA are isopropanol and ethanol to precipitate the DNA, and phenol:chloroform mixtures to extract proteins away from the DNA. I always resuspend the precipitated DNA in an aqueous solvent, sometimes just nuclease free water. It's not the best storage solution, but I don't have to store it forever. – user137 Jun 28 '15 at 22:57
  • The question received a -1. Do folk see it as being too broad, or simply unclear as it stands? – James Jun 29 '15 at 12:56
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    I'd like your reference for claiming that many DNA solutions contain organic solvents, Aside from extraction and clean-up procedures which utilize the differential solubility of cellular components to isolate DNA, most laboratory procedures (all of them that utilize DNA + enzyme reactions) are performed in aqueous solutions. While there are a few exceptions (highly concentrated synthesized oligonucleotides, perhaps large quantities of genomic DNA in a low volume), DNA is soluble in water at relevant storage and working concentrations for the vast majority molecular biology experiments. – InactionPotential Jun 29 '15 at 13:10
  • Isolated DNA and RNA are stored in water or Tris-EDTA for the reasons mdperry mentioned. The addition of other solutes to various reactions (ATP, Mg2+, various buffers, etc) is to provide for the enzyme acting upon DNA. Enzyme activity can be highly dependent on temperate, salt concentrations, pH, etc. The concentrations and compositions of the substrates and salts added to reactions involving DNA are optimized for enzyme activity. – InactionPotential Jun 29 '15 at 13:17
  • @InactionPotential I see the problem. I think I put focus on the wrong thing and perhaps semantically called additives solvents (which is incorrect). I'll edit this to remove any inaccuracies. I'm simply asking why pure water seems to not be used (and according to mdperry, ssDNA is temporarily in pure water). – James Jun 29 '15 at 13:17

2 Answers2

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DNA in pure water.

The only time that nucleic acids would encounter pure water would be in a laboratory setting--for example after an oligonucleotide is synthesized in vitro, the protecting groups are removed from the reactive atoms in the finished sequence and the final product is cleaved from the supporting matrix. At that point you can lyophilize (freeze dry) the ammonium hydroxide solution, and resuspend the single-stranded oligo in pure water.

Additional compounds enhance heavy oligomer solubility.

However, as noted in the comments, nucleic acid solubility, particularly high molecular weight DNA, like genomic DNA, is enhanced in solutions with dilute monovalent cations. 10 mM TrisHCl, pH 8.0, 1 mM EDTA suffices for almost every application. The EDTA inhibits any errant DNAses, and also slightly inhibits microbial growth.

Compounds act as pH buffers.

Tris is not the best biological buffer but has high solubility and is relatively cheap and stable. If the solution becomes too basic the DNA strands will melt, and if the solution becomes too acidic the purines will start to deaminate.

DNA never experiences pure water in biology.

From the moment that DNA is synthesized in a cell until that cell dies and its DNA is ultimately degraded, it does not encounter a pure water environment.

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mdperry
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  • Good explanation. I would reiterate in your answer (in addition to your comment above) that DNA is maintained and used in an aqueous solution. Organic solvents (phenol:chloroform) are used primarily to separate DNA from other water soluble cellular components (proteins, RNA). PCR and its variants, restrictions digests, thymidine kinase... reactions of interest performed on DNA in the laboratory are performed in aqueous solutions, they may utilize different buffers to maximize enzyme activity, but water is the solvent. – InactionPotential Jun 29 '15 at 11:56
  • This answer does an excellent job at explaining a lot about why other compounds are important and when DNA might be in pure water. It's odd to see that even ssDNA appears in pure water. Exactly what I wanted to see, thanks! – James Jun 29 '15 at 13:25
  • I've added some headers. Feel free to roll back if you want. – James Jun 29 '15 at 13:29
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    And as user137 said, DNA does dissolve in pure water. I dissolve PCR products in nuclease free water sometimes (especially if I need huge amounts of the sample for some downstream step). – WYSIWYG Jun 29 '15 at 13:47
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While physiological experiments could be conducted without organic solvents, chemical syntheses of DNA or analogs, chemical modification of DNA, and purification after chemical reaction could be performed in the presence of organic solvents. Such experiments are not directly relevant to physiology, but we use chemically synthesized DNA and DNA analogs. In addition, chemical properties of DNA in the presence of organic solvents may tell how DNA behave in physiological conditions. People doing PCR and/or molecular biology may not be interested in the solubility of DNA, because under the condition they are using, the concentrations are far less than the saturated condition.

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