Polyacrylamide (IUPAC poly(2-propenamide) or poly(1-carbamoylethylene), abbreviated as PAM) is a polymer (-CH2CHCONH2-) formed from acrylamide subunits. It can be synthesized as a simple linear-chain structure or cross-linked, typically using N,N'-methylenebisacrylamide. In the cross-linked form, the possibility of the monomer being present is reduced even further. It is highly water-absorbent, forming a soft gel when hydrated, used in such applications as polyacrylamide gel electrophoresis, and can also be called ghost crystals when cross-linked, and in manufacturing soft contact lenses. In the straight-chain form, it is also used as a thickener and suspending agent. More recently, it has been used as a subdermal filler for aesthetic facial surgery (see Aquamid).

IUPAC name
  • none
ECHA InfoCard 100.118.050
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).

Uses of polyacrylamide

One of the largest uses for polyacrylamide is to flocculate solids in a liquid. This process applies to water treatment, and processes like paper making and screen printing. Polyacrylamide can be supplied in a powder or liquid form, with the liquid form being subcategorized as solution and emulsion polymer. Even though these products are often called 'polyacrylamide', many are actually copolymers of acrylamide and one or more other chemical species, such as an acrylic acid or a salt thereof. The main consequence of this is to give the 'modified' polymer a particular ionic character.

Another common use of polyacrylamide and its derivatives is in subsurface applications such as Enhanced Oil Recovery. High viscosity aqueous solutions can be generated with low concentrations of polyacrylamide polymers, and these can be injected to improve the economics of conventional waterflooding.

The linear soil conditioning form was developed in the 1950s by Monsanto Company and was marketed under the trade name Krilium. The soil conditioning technology was presented at a symposium on "Improvement of Soil Structure" held in Philadelphia, Pennsylvania on December 29, 1951. The technology was strongly documented and was published in the June 1952 issue of the journal Soil Science, volume 73, June 1952 that was dedicated to polymeric soil conditioners.

The original formulation of Krilium was difficult to use because it contained calcium which cross-linked the linear polymer under field conditions. Even with a strong marketing campaign, Krilium was abandoned by Monsanto.

After 34 years, the journal Soil Science wanted to update the soil conditioning technology and published another dedicated issue on polymeric soil conditioner and especially linear, water-soluble, anionic polyacrylamide in the May 1986 issue, volume 141, issue number 5.

The Foreword, written by Arthur Wallace from UCLA and Sheldon D. Nelson from BYU stated in part:

The new water-soluble soil conditioners may, if used according to established procedures

  1. increase pore space in soils containing clay
  2. increase water infiltration into soils containing clay
  3. prevent soil crusting
  4. stop erosion and water runoff
  5. make friable soil that is easy to cultivate
  6. make soil dry quicker after rain or irrigation, so that the soil can be worked sooner

Consequently, these translate into

  1. stronger, larger plants with more extensive root system
  2. earlier seed emergence and crop maturity
  3. more efficient water utilization
  4. easier weed removal
  5. more response to fertilizers and to new crop varieties
  6. less plant diseases related to poor soil aeration
  7. decreased energy requirement for tillage

The cross-linked form which retains water is often used for horticultural and agricultural under trade names such as Broadleaf P4, Swell-Gel, and so on.

The anionic form of linear, water-soluble polyacrylamide is frequently used as a soil conditioner on farm land and construction sites for erosion control, in order to protect the water quality of nearby rivers and streams.[1]

The polymer is also used to make Gro-Beast toys, which expand when placed in water, such as the Test Tube Aliens. Similarly, the absorbent properties of one of its copolymers can be utilized as an additive in body-powder.

The ionic form of polyacrylamide has found an important role in the potable water treatment industry. Trivalent metal salts, like ferric chloride and aluminum chloride, are bridged by the long polymer chains of polyacrylamide. This results in significant enhancement of the flocculation rate. This allows water treatment plants to greatly improve the removal of total organic content (TOC) from raw water.

Polyacrylamide is also often used in molecular biology applications as a medium for electrophoresis of proteins and nucleic acids in a technique known as PAGE.

It was also used in the synthesis of the first Boger fluid.

Molecular biology laboratories

Polyacrylamide was first used in a laboratory setting in the early 1950s. In 1959, the groups of Davis and Ornstein[2] and of Raymond and Weintraub[3] independently published on the use of polyacrylamide gel electrophoresis to separate charged molecules.[3] The technique is widely accepted today, and remains a common protocol in molecular biology labs.

Acrylamide has many other uses in molecular biology laboratories, including the use of linear polyacrylamide (LPA) as a carrier, which aids in the precipitation of small amounts of DNA. Many laboratory supply companies sell LPA for this use.[4]

Other uses

The majority of acrylamide is used to manufacture various polymers.[5][6] In the 1970s and 1980s, the proportionately largest use of these polymers was in water treatment.[7] Additional uses include as binding, thickening or flocculating agents in grout, cement, sewage/wastewater treatment, pesticide formulations, cosmetics, sugar manufacturing, soil erosion prevention, ore processing, food packaging, plastic products, and paper production.[5][8] Polyacrylamide is also used in some potting soil.[5] Another use of polyacrylamide is as a chemical intermediate in the production of N-methylol acrylamide and N-butoxyacrylamide.[8] In oil and gas industry Polyacrylamide derivatives especially co-polymers of that have a substantial effect on unconventional production and hydraulic fracturing. As an nonionic monomer it can be co-polymerize with anionic for example Acrylic acid and cationic monomer such as diallyldimethyl ammonium chloride (DADMAC) and resulted co-polymer that can have different compatibility in different applications.

Soil conditioner

The primary functions of polyacrylamide soil conditioners are to increase soil tilth, aeration, and porosity and reduce compaction, dustiness and water run-off. Secondary functions are to increase plant vigor, color, appearance, rooting depth and emergence of seeds while decreasing water requirements, diseases, erosion and maintenance expenses. FC 2712 is used for this purpose.


In dilute aqueous solution, such as is commonly used for Enhanced Oil Recovery applications, polyacrylamide polymers are susceptible to chemical, thermal, and mechanical degradation. Chemical degradation occurs when the labile amide moiety hydrolyzes at elevated temperature or pH, resulting in the evolution of ammonia and a remaining carboxyl group. Thus, the degree of anionicity of the molecule increases. Thermal degradation of the vinyl backbone can occur through several possible radical mechanisms, including the autooxidation of small amounts of iron and reactions between oxygen and residual impurities from polymerization at elevated temperature. Mechanical degradation can also be an issue at the high shear rates experienced in the near-wellbore region.

Environmental effects

Concerns have been raised that polyacrylamide used in agriculture may contaminate food with acrylamide, a known neurotoxin and carcinogen.[9] While polyacrylamide itself is relatively non-toxic, it is known that commercially available polyacrylamide contains minute residual amounts of acrylamide remaining from its production, usually less than 0.05% w/w.[10]

Additionally, there are concerns that polyacrylamide may de-polymerise to form acrylamide. In a study conducted in 2003 at the Central Science Laboratory in Sand Hutton, England, polyacrylamide was treated similarly as food during cooking. It was shown that these conditions do not cause polyacrylamide to de-polymerise significantly.[11]

In a study conducted in 1997 at Kansas State University, the effect of environmental conditions on polyacrylamide were tested, and it was shown that degradation of polyacrylamide under certain conditions can cause the release of acrylamide.[12] The experimental design of this study as well as its results and their interpretation have been questioned,[13][14] and a 1999 study by the Nalco Chemical Company did not replicate the results.[15]

See also


  1. ^ Construction Contract Standards [1] "Standard Specifications State of California"
  2. ^ Davis and Ornstein Archived 2011-09-26 at the Wayback Machine. Pipeline.com. Retrieved on 2012-06-11.
  3. ^ a b Reynolds S, Weintraub L (18 September 1959). "Acrylamide Gel as a Supporting Medium for Zone Electrophoresis". Science. 130 (3377): 711. doi:10.1126/science.130.3377.711. PMID 14436634.
  4. ^ GenElute™-LPA from Sigma-Aldrich. biocompare.com
  5. ^ a b c Environment Canada; Health Canada (August 2009). "Screening Assessment for the Challenge: 2-Propenamide (Acrylamide)". Environment and Climate Change Canada. Government of Canada.
  6. ^ Office of Pollution Prevention and Toxics (September 1994). "II. Production, Use, and Trends". Chemical Summary for Acrylamide (plain text) (Report). United States Environmental Protection Agency. EPA 749-F-94-005a. Retrieved November 30, 2013.
  7. ^ "Polyacrylamide". Hazardous Substances Data Bank. United States National Library of Medicine. February 14, 2003. Consumption Patterns. CASRN: 9003-05-8. Retrieved November 30, 2013.
  8. ^ a b Dotson, GS (April 2011). "NIOSH skin notation (SK) profile: acrylamide [CAS No. 79-06-1]" (PDF). DHHS (NIOSH) Publication No. 2011-139. National Institute for Occupational Safety and Health (NIOSH).
  9. ^ https://www.cdc.gov/niosh/docs/2011-139/pdfs/2011-139.pdf
  10. ^ Woodrow JE; Seiber JN; Miller GC. (Apr 23, 2008). "Acrylamide Release Resulting from Sunlight Irradiation of Aqueous Polyacrylamide/Iron Mixtures". Journal of Agricultural and Food Chemistry. 56 (8): 2773–2779. doi:10.1021/jf703677v.
  11. ^ Ahn JS; Castle L. (5 November 2003). "Tests for the Depolymerization of Polyacrylamides as a Potential Source of Acrylamide in Heated Foods". Journal of Agricultural and Food Chemistry. 51 (23). doi:10.1021/jf0302308.
  12. ^ Smith EA; Prues SL; Oehme FW. (June 1997). "Environmental degradation of polyacrylamides. II. Effects of environmental (outdoor) exposure". Ecotoxicology and Environmental Safety. 37 (1): 76–91. doi:10.1006/eesa.1997.1527.
  13. ^ Kay-Shoemake JL; Watwood ME; Lentz RD; Sojka RE. (August 1998). "Polyacrylamide as an organic nitrogen source for soil microorganisms with potential effects on inorganic soil nitrogen in agricultural soil". Soil Biology and Biochemistry. 30 (8/9): 1045–1052. doi:10.1016/S0038-0717(97)00250-2.
  14. ^ Gao JP; Lin T; Wang W; Yu JG; Yuan SJ; Wang SM. (1999). "Accelerated chemical degradation of polyacrylamide". Macromolecular Symposia. 144: 179–185. ISSN 1022-1360.
  15. ^ Ver Vers LM. (December 1999). "Determination of acrylamide monomer in polyacrylamide degradation studies by high-performance liquid chromatography". Journal of Chromatographic Science. 37 (12): 486–494.
Affinity electrophoresis

Affinity electrophoresis is a general name for many analytical methods used in biochemistry and biotechnology. Both qualitative and quantitative information may be obtained through affinity electrophoresis. The methods include the so-called electrophoretic mobility shift assay, charge shift electrophoresis and affinity capillary electrophoresis. The methods are based on changes in the electrophoretic pattern of molecules (mainly macromolecules) through biospecific interaction or complex formation. The interaction or binding of a molecule, charged or uncharged, will normally change the electrophoretic properties of a molecule. Membrane proteins may be identified by a shift in mobility induced by a charged detergent. Nucleic acids or nucleic acid fragments may be characterized by their affinity to other molecules. The methods have been used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding. For enzymes and other ligand-binding proteins, one-dimensional electrophoresis similar to counter electrophoresis or to "rocket immunoelectrophoresis", affinity electrophoresis may be used as an alternative quantification of the protein. Some of the methods are similar to affinity chromatography by use of immobilized ligands.

Body powder

Body powder is the generic name for alternatives to talcum powder. It is usually made from a combination of tapioca flour, rice flour, cornstarch, kaolin, arrowroot powder, and/or orrisroot powder, but also other powders may be used. In addition, water absorbing and water binding agents may be added such as polyacrylamide.

Coomassie Brilliant Blue

Coomassie Brilliant Blue is the name of two similar triphenylmethane dyes that were developed for use in the textile industry but are now commonly used for staining proteins in analytical biochemistry. Coomassie Brilliant Blue G-250 differs from Coomassie Brilliant Blue R-250 by the addition of two methyl groups. The name "Coomassie" is a registered trademark of Imperial Chemical Industries.


Counterimmunoelectrophoresis is a laboratory technique used to evaluate the binding of an antibody to its antigen, it is similar to immunodiffusion, but with the addition of an applied electrical field across the diffusion medium, usually an agar or polyacrylamide gel. The effect is rapid migration of the antibody and antigen out of their respective wells towards one another to form a line of precipitation, or a precipitin line, indicating binding.

Discontinuous electrophoresis

Discontinuous electrophoresis (colloquially disc electrophoresis) is a type of polyacrylamide gel electrophoresis. It was developed by Ornstein and Davis. This method produces high resolution and good band definition. It is widely used technique for separating proteins according to size and charge.


Electroblotting is a method in molecular biology/biochemistry/immunogenetics to transfer proteins or nucleic acids onto a membrane by using PVDF or nitrocellulose, after gel electrophoresis. The protein or nucleic acid can then be further analyzed using probes such as specific antibodies, ligands like lectins, or stains. This method can be used with all polyacrylamide and agarose gels. An alternative technique for transferring proteins from a gel is capillary blotting.

Gel electrophoresis

Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF agarose, essentially size independent) and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through a matrix of agarose or other substances. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving. Proteins are separated by charge in agarose because the pores of the gel are too large to sieve proteins. Gel electrophoresis can also be used for separation of nanoparticles.

Gel electrophoresis uses a gel as an anticonvective medium or sieving medium during electrophoresis, the movement of a charged particle in an electrical field. Gels suppress the thermal convection caused by application of the electric field, and can also act as a sieving medium, retarding the passage of molecules; gels can also simply serve to maintain the finished separation, so that a post electrophoresis stain can be applied. DNA Gel electrophoresis is usually performed for analytical purposes, often after amplification of DNA via polymerase chain reaction (PCR), but may be used as a preparative technique prior to use of other methods such as mass spectrometry, RFLP, PCR, cloning, DNA sequencing, or Southern blotting for further characterization.

Gel electrophoresis of proteins

Protein electrophoresis is a method for analysing the proteins in a fluid or an extract. The electrophoresis may be performed with a small volume of sample in a number of alternative ways with or without a supporting medium: SDS polyacrylamide gel electrophoresis (in short: gel electrophoresis, PAGE, or SDS-electrophoresis), free-flow electrophoresis, electrofocusing, isotachophoresis, affinity electrophoresis, immunoelectrophoresis, counterelectrophoresis, and capillary electrophoresis. Each method has many variations with individual advantages and limitations. Gel electrophoresis is often performed in combination with electroblotting immunoblotting to give additional information about a specific protein. Because of practical limitations, protein electrophoresis is generally not suited as a preparative method.

Isoelectric point

The isoelectric point (pI, pH(I), IEP), is the pH at which a particular molecule carries no net electrical charge or is electrically neutral in the statistical mean. The standard nomenclature to represent the isoelectric point is pH(I), although pI is also commonly seen, and is used in this article for brevity. The net charge on the molecule is affected by pH of its surrounding environment and can become more positively or negatively charged due to the gain or loss, respectively, of protons (H+).

Surfaces naturally charge to form a double layer. In the common case when the surface charge-determining ions are H+/OH−, the net surface charge is affected by the pH of the liquid in which the solid is submerged.

The pI value can affect the solubility of a molecule at a given pH. Such molecules have minimum solubility in water or salt solutions at the pH that corresponds to their pI and often precipitate out of solution. Biological amphoteric molecules such as proteins contain both acidic and basic functional groups. Amino acids that make up proteins may be positive, negative, neutral, or polar in nature, and together give a protein its overall charge. At a pH below their pI, proteins carry a net positive charge; above their pI they carry a net negative charge. Proteins can, thus, be separated by net charge in a polyacrylamide gel using either preparative gel electrophoresis, which uses a constant pH to separate proteins or isoelectric focusing, which uses a pH gradient to separate proteins. Isoelectric focusing is also the first step in 2-D gel polyacrylamide gel electrophoresis.

In biomolecules, proteins can be separated by ion exchange chromatography. Biological proteins are made up of zwitterionic amino acid compounds; the net charge of these proteins can be positive or negative depending on the pH of the environment. The specific pI of the target protein can be used to model the process around and the compound can then be purified from the rest of the mixture. Buffers of various pH can be used for this purification process to change the pH of the environment. When a mixture containing a target protein is loaded into an ion exchanger, the stationary matrix can be either positively-charged (for mobile anions) or negatively-charged (for mobile cations). At low pH values, the net charge of most proteins in the mixture is positive - in cation exchangers, these positively-charged proteins bind to the negatively-charged matrix. At high pH values, the net charge of most proteins is negative, where they bind to the positively-charged matrix in anion exchangers. When the environment is at a pH value equal to the protein's pI, the net charge is zero, and the protein is not bound to any exchanger, and therefore, can be eluted out.


N,N'-Methylenebisacrylamide (MBAm or MBAA) is a cross-linking agent used during the formation of polymers such as polyacrylamide. Its molecular formula is C7H10N2O2. Bisacrylamide is used in biochemistry as it is one of the compounds of the polyacrylamide gel (used for SDS-PAGE). Bisacrylamide polymerizes with acrylamide and is capable of creating cross-links between polyacrylamide chains, thus creating a network of polyacrylamide rather than unconnected linear chains of polyacrylamide.

Polyacrylamide gel electrophoresis

Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after electrophoresis, it provides information on the sample composition of the RNA species.Hydration of acrylonitrile results in formation of acrylamide molecules (C3H5NO) by nitrile hydratase. Acrylamide monomer is in a powder state before addition of water. Acrylamide is toxic to the human nervous system, therefore all safety measures must be followed when working with it. Acrylamide is soluble in water and upon addition of water it polymerizes resulting in formation of polyacrylamide. It is useful to make polyacrylamide gel via acrylmide hydration because pore size can be regulated. Increased concentrations of acrylamide result in decreased pore size after polymerization. Polyacrylamide gel with small pores helps to examine smaller molecules better since the small molecules can enter the pores and travel through the gel while large molecules get trapped at the pore openings.

As with all forms of gel electrophoresis, molecules may be run in their native state, preserving the molecules' higher-order structure. This method is called native-PAGE. Alternatively, a chemical denaturant may be added to remove this structure and turn the molecule into an unstructured molecule whose mobility depends only on its length (because the protein-SDS complexes all have a similar mass-to-charge ratio). This procedure is called SDS-PAGE. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is a method of separating molecules based on the difference of their molecular weight. At the pH at which gel electrophoresis is carried out the SDS molecules are negatively charged and bind to proteins in a set ratio, approximately one molecule of SDS for every 2 amino acids. In this way, the detergent provides all proteins with a uniform charge-to-mass ratio. By binding to the proteins the detergent destroys their secondary, tertiary and/or quaternary structure denaturing them and turning them into negatively charged linear polypeptide chains. When subjected to an electric field in PAGE, the negatively charged polypeptide chains travel toward the anode with different mobility. Their mobility, or the distance traveled by molecules, is inversely proportional to the logarithm of their molecular weight. By comparing the relative ratio of the distance traveled by each protein to the length of the gel (Rf) one can make conclusions about the relative molecular weight of the proteins, where the length of the gel is determined by the distance traveled by a small molecule like a tracking dye.For nucleic acids, urea is the most commonly used denaturant. For proteins, sodium dodecyl sulfate (SDS) is an anionic detergent applied to protein samples to coat proteins in order to impart two negative charges (from every SDS molecule) to every two amino acids of the denatured protein. 2-Mercaptoethanol may also be used to disrupt the disulfide bonds found between the protein complexes, which helps further denature the protein. In most proteins, the binding of SDS to the polypeptide chains impart an even distribution of charge per unit mass, thereby resulting in a fractionation by approximate size during electrophoresis. Proteins that have a greater hydrophobic content — for instance, many membrane proteins, and those that interact with surfactants in their native environment — are intrinsically harder to treat accurately using this method, due to the greater variability in the ratio of bound SDS. Procedurally, using both Native and SDS-PAGE together can be used to purify and to separate the various subunits of the protein. Native-PAGE keeps the oligomeric form intact and will show a band on the gel that is representative of the level of activity. SDS-PAGE will denature and separate the oligomeric form into its monomers, showing bands that are representative of their molecular weights. These bands can be used to identify and assess the purity of the protein.

Polyacrylic acid

Poly(acrylic acid) (PAA; trade name Carbomer) is a synthetic high-molecular weight polymer of acrylic acid. The IUPAC name is poly(1-carboxyethylene. They may be homopolymers of acrylic acid, or crosslinked with an allyl ether of pentaerythritol, allyl ether of sucrose, or allyl ether of propylene. In a water solution at neutral pH, PAA is an anionic polymer, i.e. many of the side chains of PAA will lose their protons and acquire a negative charge. This makes PAAs polyelectrolytes, with the ability to absorb and retain water and swell to many times their original volume. Dry PAAs are sold as white, fluffy powders that are frequently used as gels in cosmetic and personal care products. Their role in cosmetics is to suspend solid in liquids, prevent emulsions from separating and control the consistency in flow of cosmetics. Carbomer codes (910, 934, 940, 941, and 934P) are an indication of molecular weight and the specific components of the polymer. For many applications PAAs are used in form of alkali metal or ammonium salts, e.g. sodium polyacrylate.

In the dry powder form, the positively charged sodium ions are bound to the polyacrylate. However, in aqueous solutions the sodium ions are free to move since they are replaced by positively charged hydrogen ions. Instead of an organized polymer chain, this leads to a swollen gel that can absorb a high amount of water.

Polyacrylic acid is a weak anionic polyelectrolyte, whose degree of ionisation is dependent on solution pH. In its non-ionised form at low pHs, PAA may associate with various non-ionic polymers (such as polyethylene oxide, poly-N-vinyl pyrrolidone, polyacrylamide, and some cellulose ethers) and form hydrogen-bonded interpolymer complexes. In aqueous solutions PAA can also form polycomplexes with oppositely charged polymers (for example, chitosan), surfactants, and drug molecules (for example, streptomycin).


QPNC-PAGE, or quantitative preparative native continuous polyacrylamide gel electrophoresis, is a bioanalytical, high-resolution and highly accurate technique applied in biochemistry and bioinorganic chemistry to separate proteins quantitatively by isoelectric point. This standardized variant of native gel electrophoresis is used by biologists to isolate biomacromolecules in solution, for example, active or native metalloproteins in biological samples or properly and improperly folded metal cofactor-containing proteins or protein isoforms in complex protein mixtures.


SDS-PAGE (sodium dodecyl sulfate–polyacrylamide gel electrophoresis) is a variant of polyacrylamide gel electrophoresis, an analytical method in biochemistry for the separation of charged molecules in mixtures by their molecular masses in an electric field. It uses sodium dodecyl sulfate (SDS) molecules to help identify and isolate protein molecules.

SDS-PAGE is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 KDa. The publication describing it is the most frequently cited paper by a single author, and the second most cited overall.

Silver staining

Silver staining is the use of silver to selectively alter the appearance of a target in microscopy of histological sections; in temperature gradient gel electrophoresis; and in polyacrylamide gels.

Southwestern blot

Southwestern blotting, based along the lines of Southern blotting (which was created by Edwin Southern) and first described by B. Bowen, J. Steinberg and colleagues in 1980, is a lab technique which involves identifying and characterizing DNA-binding proteins (proteins that bind to DNA) by their ability to bind to specific oligonucleotide probes. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes, similar to other types of blotting.

The name southwestern blotting is based on the fact that this technique detects DNA-binding proteins, since DNA detection is by Southern blotting and protein detection is by western blotting.

However, since the first southwestern blottings, many more have been proposed and discovered. The former protocols were hampered by the need for large amounts of proteins and their susceptibility to degradation while being isolated.

"Southwestern blot mapping" is performed for rapid characterization of both DNA-binding proteins and their specific sites on genomic DNA. Proteins are separated on a polyacrylamide gel (PAGE) containing sodium dodecyl sulfate (SDS), renatured by removing SDS in the presence of urea, and blotted onto nitrocellulose by diffusion. The genomic DNA region of interest is digested by restriction enzymes selected to produce fragments of appropriate but different sizes, which are subsequently end-labeled and allowed to bind to the separated proteins. The specifically-bound DNA is eluted from each individual protein-DNA complex and analyzed by polyacrylamide gel electrophoresis. Evidence that tissue-specific DNA binding proteins may be detected by this technique has been presented. Moreover, their sequence-specific binding allows the purification of the corresponding selectively bound DNA fragments and may improve protein-mediated cloning of DNA regulatory sequences.

Water gel (plain)

Water crystal gel or water beads is any gel which contains a large amount of water. Water gel is usually composed of a water-absorbing polymer such as a polyacrylamide (frequently Poly(methyl acrylate) or Sodium polyacrylate). Sometimes referred to as superabsorbent polymer (SAP) or, in dry form, as slush powder.

Xylene cyanol

Xylene cyanol can be used as a color marker, or tracking dye, to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Bromophenol blue and orange G can also be used for this purpose.

Once mixed with the sample, the concentration of xylene cyanol is typically about 0.005% to 0.03%.

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