ethanol precipitation
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Ethanol precipitation is a method used to purify and/or concentrate
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
, DNA, and
polysaccharide Polysaccharides (), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with wa ...
s such as
pectin Pectin ( grc, πηκτικός ': "congealed" and "curdled") is a heteropolysaccharide, a structural acid contained in the primary lamella, in the middle lamella, and in the cell walls of terrestrial plants. The principal, chemical component of ...
and
xyloglucan Xyloglucan is a hemicellulose that occurs in the primary cell wall of all vascular plants; however, all enzymes responsible for xyloglucan metabolism are found in Charophyceae algae.LEV Del Bem and M Vincentz (2010) Evolution of xyloglucan-relate ...
from
aqueous solutions An aqueous solution is a solution in which the solvent is water. It is mostly shown in chemical equations by appending (aq) to the relevant chemical formula. For example, a solution of table salt, or sodium chloride (NaCl), in water would be rep ...
by adding
ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an Alcohol (chemistry), alcohol with the chemical formula . Its formula can be also written as or (an ethyl ...
as an antisolvent.


DNA precipitation


Theory

DNA is
polar Polar may refer to: Geography Polar may refer to: * Geographical pole, either of two fixed points on the surface of a rotating body or planet, at 90 degrees from the equator, based on the axis around which a body rotates * Polar climate, the c ...
due to its highly charged
phosphate In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthophosphoric acid . The phosphate or orthophosphate ion is derived from phospho ...
backbone. Its polarity makes it water-soluble (water is polar) according to the principle "like dissolves like". Because of the high polarity of water, illustrated by its high
dielectric constant The relative permittivity (in older texts, dielectric constant) is the permittivity of a material expressed as a ratio with the electric permittivity of a vacuum. A dielectric is an insulating material, and the dielectric constant of an insulat ...
of 80.1 (at 20 °C), electrostatic forces between
charged particles In physics, a charged particle is a particle with an electric charge. It may be an ion, such as a molecule or atom with a surplus or deficit of electrons relative to protons. It can also be an electron or a proton, or another elementary particle, ...
are considerably lower in aqueous solution than they are in a
vacuum A vacuum is a space devoid of matter. The word is derived from the Latin adjective ''vacuus'' for "vacant" or "void". An approximation to such vacuum is a region with a gaseous pressure much less than atmospheric pressure. Physicists often dis ...
or in air. This relation is reflected in
Coulomb's law Coulomb's inverse-square law, or simply Coulomb's law, is an experimental law of physics that quantifies the amount of force between two stationary, electrically charged particles. The electric force between charged bodies at rest is conventiona ...
, which can be used to calculate the force acting on two charges q_1 and q_2 separated by a distance r by using the dielectric constant \varepsilon_r (also called relative static permittivity) of the medium in the denominator of the equation (\varepsilon_0 is an
electric constant Vacuum permittivity, commonly denoted (pronounced "epsilon nought" or "epsilon zero"), is the value of the absolute dielectric permittivity of classical vacuum. It may also be referred to as the permittivity of free space, the electric const ...
): F = \frac \frac At an atomic level, the reduction in the force acting on a charge results from water molecules forming a hydration shell around it. This fact makes water a very good solvent for charged compounds like salts. Electric force which normally holds salt
crystal A crystal or crystalline solid is a solid material whose constituents (such as atoms, molecules, or ions) are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions. In addition, macros ...
s together by way of
ionic bonds Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities, and is the primary interaction occurring in ionic compounds. ...
is weakened in the presence of water allowing ions to separate from the crystal and spread through solution. The same mechanism operates in the case of negatively charged phosphate groups on a DNA backbone: even though positive ions are present in solution, the relatively weak net electrostatic force prevents them from forming stable ionic bonds with phosphates and
precipitating In an aqueous solution, precipitation is the process of transforming a dissolved chemical substance, substance into an insoluble solid from a Supersaturated solution, super-saturated solution. The solid formed is called the precipitate. In cas ...
out of solution.
Ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an Alcohol (chemistry), alcohol with the chemical formula . Its formula can be also written as or (an ethyl ...
is much less polar than water, with a dielectric constant of 24.3 (at 25 °C). This means that adding ethanol to solution disrupts the screening of charges by water. If enough ethanol is added, the electrical attraction between phosphate groups and any positive ions present in solution becomes strong enough to form stable
ionic bonds Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities, and is the primary interaction occurring in ionic compounds. ...
and DNA precipitation. This usually happens when ethanol composes over 64% of the solution. As the mechanism suggests, the solution has to contain positive ions for precipitation to occur; usually Na+, NH4+ or Li+ plays this role .Molecular Cloning: A Laboratory Manual (Third Edition) by Joseph Sambrook, Peter MacCallum Cancer Institute, Melbourne, Australia; David Russell, University of Texas Southwestern Medical Center, Dallas


Practice

DNA is precipitated by first ensuring that the correct concentration of positive ions is present in solution (too much will result in a lot of salt co-precipitating with DNA, too little will result in incomplete DNA recovery) and then adding two to three volumes of at least 95% ethanol. Many protocols advise storing DNA at low temperature at this point, but there are also observations that it may not improve DNA recovery, and may even lower precipitation efficiency while using over-night incubation time. Therefore, good efficiency can be achieved at room temperature, but when possible degradation is taken into account, it is probably better to incubate DNA on wet ice. Optimal incubation time depends on the length and concentration of DNA. Smaller fragments and lower concentrations will require longer times to achieve acceptable recovery. For very small lengths and low concentrations over-night incubation is recommended. In such cases use of carriers like
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ac ...
,
glycogen Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. The polysaccharide structure represents the main storage form of glucose in the body. Glycogen functions as one o ...
or linear
polyacrylamide Polyacrylamide (abbreviated as PAM) is a polymer with the formula (-CH2CHCONH2-). It has a linear-chain structure. PAM is highly water-absorbent, forming a soft gel when hydrated. In 2008, an estimated 750,000,000 kg were produced, mainly f ...
can greatly improve recovery. During incubation DNA and some salts will precipitate from solution, in the next step this precipitate is collected by
centrifugation Centrifugation is a mechanical process which involves the use of the centrifugal force to separate particles from a solution according to their size, shape, density, medium viscosity and rotor speed. The denser components of the mixture migrate ...
in a microcentrifuge tube at high speeds (~12,000 g). Time and speed of centrifugation has the biggest effect on DNA recovery rates. Again smaller fragments and higher dilutions require longer and faster centrifugation. Centrifugation can be done either at room temperature or in 4 °C or 0 °C. During centrifugation precipitated DNA has to move through ethanol solution to the bottom of the tube, lower temperatures increase
viscosity The viscosity of a fluid is a measure of its resistance to deformation at a given rate. For liquids, it corresponds to the informal concept of "thickness": for example, syrup has a higher viscosity than water. Viscosity quantifies the inte ...
of the solution and larger volumes make the distance longer, so both those factors lower efficiency of this process requiring longer centrifugation for the same effect. After centrifugation the supernatant solution is removed, leaving a ''pellet'' of crude DNA. Whether the pellet is visible depends on the amount of DNA and on its purity (dirtier pellets are easier to see) or the use of co-precipitants. In the next step, 70% ethanol is added to the pellet, and it is gently mixed to break the pellet loose and wash it. This removes some of the salts present in the leftover supernatant and bound to DNA pellet making the final DNA cleaner. This suspension is centrifuged again to once again pellet DNA and the supernatant solution is removed. This step is repeated once. Finally, the pellet is air-dried and the DNA is resuspended in water or other desired
buffer Buffer may refer to: Science * Buffer gas, an inert or nonflammable gas * Buffer solution, a solution used to prevent changes in pH * Buffering agent, the weak acid or base in a buffer solution * Lysis buffer, in cell biology * Metal ion buffer * ...
. It is important not to over-dry the pellet as it may lead to denaturation of DNA and make it harder to resuspend.
Isopropanol Isopropyl alcohol (IUPAC name propan-2-ol and also called isopropanol or 2-propanol) is a colorless, flammable organic compound with a pungent alcoholic odor. As an isopropyl group linked to a hydroxyl group (chemical formula ) it is the simple ...
can also be used instead of ethanol; the precipitation efficiency of the isopropanol is higher making one volume enough for precipitation. However, isopropanol is less volatile than ethanol and needs more time to air-dry in the final step. The pellet might also adhere less tightly to the tube when using isopropanol.


See also

*
DNA extraction The first isolation of deoxyribonucleic acid (DNA) was done in 1869 by Friedrich Miescher. Currently, it is a routine procedure in molecular biology or forensic analyses. For the chemical method, many different kits are used for extraction, and s ...
*
Phenol–chloroform extraction Phenol–chloroform extraction is a liquid-liquid extraction technique in molecular biology used to separate nucleic acids from proteins and lipids. Process Aqueous samples, lysed cells, or homogenised tissue are mixed with equal volumes of a pheno ...
*
Salting in Salting in refers to the effect where increasing the ionic strength of a solution increases the solubility of a solute, such as a protein. This effect tends to be observed at lower ionic strengths. Protein solubility is a complex function of p ...
*
Salting out Salting out (also known as salt-induced precipitation, salt fractionation, anti-solvent crystallization, precipitation crystallization, or drowning out) is a purification technique that utilizes the reduced solubility of certain molecules in a s ...
* SCODA DNA purification *
Spin column-based nucleic acid purification Spin column-based nucleic acid purification is a solid phase extraction method to quickly purify nucleic acids. This method relies on the fact that nucleic acid will bind to the solid phase of silica under certain conditions. Procedure The stages ...


References


External links


bitesizebio.com The Basics: How Ethanol Precipitation of DNA and RNA Works
* * {{Portal bar, Biology Laboratory techniques Molecular biology