2
$\begingroup$

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?

$\endgroup$
  • 2
    $\begingroup$ 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. $\endgroup$ – March Ho Jun 28 '15 at 17:53
  • 2
    $\begingroup$ 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? $\endgroup$ – mdperry Jun 28 '15 at 18:25
  • 1
    $\begingroup$ www3.idtdna.com/pages/support/technical-vault/faq-old/… How about this. $\endgroup$ – 243 Jun 28 '15 at 21:35
  • 2
    $\begingroup$ 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? $\endgroup$ – Chris Jun 28 '15 at 21:57
  • 2
    $\begingroup$ 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. $\endgroup$ – user137 Jun 28 '15 at 22:57
5
$\begingroup$

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.

$\endgroup$
  • $\begingroup$ 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. $\endgroup$ – InactionPotential Jun 29 '15 at 11:56
  • $\begingroup$ 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! $\endgroup$ – James Jun 29 '15 at 13:25
  • $\begingroup$ I've added some headers. Feel free to roll back if you want. $\endgroup$ – James Jun 29 '15 at 13:29
  • 1
    $\begingroup$ 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). $\endgroup$ – WYSIWYG Jun 29 '15 at 13:47
0
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.