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eHow Hobbies, Games & Toys Science & Nature Science Why Is Sodium Used in DNA Extraction?

Why Is Sodium Used in DNA Extraction?

By Robin Wasserman, eHow Contributor
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DNA does not float around free inside the

nucleus of a cell. It is associated with a
variety of different proteins and encased in a
cellular membrane. In animal cells, the
DNA is also contained within a nuclear
membrane. In order to extract DNA from a
cell, the associated membranes and proteins
must first be removed and then physically
separated from the DNA. Sodium can be
involved in several of the steps to accomplish
this goal.

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Sodium as a Detergent
Sodium is an element. It's chemical symbol is Na for Natrium, the Latin word for sodium. It
is a positive ion and often associates with negative ions as part of useful compounds. For
example, when sodium ions are bound to chloride ions, they make the compound sodium
chloride, which is ordinary table salt.
Several different forms of sodium are used in DNA extraction. Sodium dodecyl sulfate, or
SDS. is a sodium-containing detergent. It has the chemical formula of C12H25NaO4S, where
the Na stands for sodium. Detergents are used to break down cell walls and membranes.
They work by chemically poking holes in the cell membranes or walls.
Once holes are poked in the membranes, the membranes can be further disrupted
mechanically, as with a blender. After that, it is easier to get the contents of the cell out,
including the DNA.

Sodium as an Alkaline Agent

Sodium hydroxide is another compound containing sodium that is used to extract DNA out of
a cell. The chemical formula for sodium hydroxide is NaOH. Sodium hydroxide is a base. A
solution of sodium hydroxide makes the solution very basic or alkaline. Sodium hydroxide
can act by loosening the rigid structure of a cell wall or membrane, thereby releasing the
DNA.
Sodium hydroxide is most often used in plasmid DNA extraction. Plasmid DNA in bacteria
usually exists in a ring form in the cytoplasm, separate from the chromosomal DNA in the
nucleus. While chromosomal DNA programs the bacterial cell's functions and processes,
plasmid DNA is often a genetically engineered DNA that codes for a specific gene or genes of
interest. Plasmids are highly valuable research tools and their extraction from bacterial cells
is a routine laboratory procedure.
To separate the bacterial chromosomal DNA and sheared DNA from plasmid DNA, sodium
hydroxide is often used. Chromosomal DNA and sheared DNA are both linear, whereas
plasmid DNA is circular. When the solution is basic, for example, when sodium hydroxide is
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added, double-stranded DNA molecules separate. This is known as denaturation. Their

complementary bases are no longer associated with each other. This can be thought of much
like the two complementary sides of a zipper. When DNA is double-stranded, the zipper is
zipped up. When the DNA is denatured, the zipper is not only unzipped, but the two strands
are completely separated from each other, like in a jacket.
On the other hand, plasmid DNA molecules, although they are unzipped, are not separated.
The circular strands can easily find their complementary strands and "renature" back into a
circular double-stranded plasmid DNA molecule once the solution is no longer alkaline. This
is one of the unique properties of plasmids that allow them to be separated from
chromosomal DNA. In this way, the plasmid DNA with the desired gene of interest can be
removed and separated from the regular bacterial chromosomal DNA.

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Sodium Acetate's Role

Sodium can also be in the form of sodium acetate. Like sodium hydroxide, sodium acetate is
used to help separate plasmid DNA from chromosomal DNA, but by a much different
mechanism and at a different part of the DNA extraction procedure.
Single strands of linear DNA are insoluble in high salt. They will precipitate out, forming a
solid. Adding sodium acetate to SDS detergent solutions forms solids of cellular debris as well
as denatured chromosomal linear DNA. Circular plasmid DNA is not insoluble in high salt.
Plasmid DNA will remain in solution, thus separating the desired plasmid DNA from the rest
of the DNA in the cell.
Sodium hydroxide provides the basic solution to denature and unzip the DNA strands, both
plasmid and chromosomal. Once the DNA is no longer in the alkaline solution, only the
plasmid DNA can zip back up. In order to separate the denatured, unzipped, chromosomal
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DNA from the renatured, zipped-up plasmid DNA, sodium acetate is used to selectively
precipitate the chromosomal DNA and other cellular debris away from the desired doublestranded plasmid DNA.

Role of Sodium in DNA Precipitation

Precipitated chromosomal DNA and cellular debris can be removed from the soluble plasmid
DNA still in solution by centrifugation, a high-speed spinning process that causes the solids to
be forced into the bottom of a tube as a small pellet, allowing the liquid at the top containing
plasmid DNA to be separated out.
This plasmid DNA can then be precipitated out of the solution by adding an alcohol and a
salt. It is often desirable to precipitate out the plasmid DNA in order to concentrate its
amount in solution and in order to bring it back up into a solution that is stabilizing to its
chemical structure. The salt used to precipitate the plasmid DNA can be sodium chloride or
sodium acetate, for example, but can also be ammonium acetate or lithium chloride.
Sodium is a positively charged ion. In a solution of sodium chloride, table salt, for example,
the sodium chloride molecule separates into sodium ions and chloride ions. DNA , on the
other hand, is highly negatively charged. The large negative charge of the DNA molecule is
neutralized by the positive sodium ions in solution. This neutralization of the negative
charges on DNA allows it to precipitate in alcohol. Without the salt, the DNA remains
negatively charged and will stay in the aqueous part of the solution.
If this mixture is centrifuged, the precipitated plasmid DNA will become a pellet at the
bottom of the tube. The liquid portion can be removed and the DNA can then be put back
into solution, or resuspended, in a different solution at the desired concentration.

Sodium as Part of the Buffer Solution

DNA is usually resuspended in a solution containing Tris and EDTA. This is called a buffer
solution. EDTA stands for the chemical ethylenediamine tetracetic acid, and usually exists in
the lab as a disodium salt, Na2C10H16N2O8. Buffers are used to prevent drastic pH changes,
and in this case, Tris/EDTA keeps the DNA in a solution in a pH range of about 7.0 to 9.0.
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References
Microbial Life Educational Resources: DNA Extraction
Evaluation of Different Methods of DNA Extraction
Merriam-Webster Online: Definition of Sodium
ChemIndustry.com: IUPAC Name for SDS

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