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SDS-PAGE
SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel
electrophoresis, is a technique widely used in
biochemistry, forensics, genetics and molecular biology to
separate proteins according to their electrophoretic mobility
(a function of length of polypeptide chain or molecular
weight). SDS gel electrophoresis of samples having
identical charge per unit mass due to binding of SDS results
in fractionation by size.
Procedure
Tissue preparation
Samples may be taken from whole tissue or from cell
culture. In most cases, solid tissues are first broken down
mechanically using a blender (for larger sample volumes),
using a homogenizer (smaller volumes), or by sonication. Picture of an SDS-PAGE. The molecular marker is in the left
Cells may also be broken open by one of the above lane
mechanical methods. However, it should be noted that
bacteria, virus or environmental samples can be the source of protein and thus Western blotting is not restricted to
cellular studies only.
A combination of biochemical and mechanical techniques – including various types of filtration and centrifugation –
can be used to separate different cell compartments and organelles.
The solution of proteins to be analyzed is mixed with SDS, an anionic detergent which denatures secondary and
non–disulfide–linked tertiary structures, and applies a negative charge to each protein in proportion to its mass.
Heating the samples to at least 60 degrees C shakes up the molecules, helping SDS to bind. [1] [2] [3] [4]
A tracking dye may be added to the protein solution (of a size smaller than protein) to allow the experimenter to
track the progress of the protein solution through the gel during the electrophoretic run.
SDS-PAGE 2
Gels are polymerized in a gel caster. First the separating gel is poured and allowed to polymerize. Next a thin layer
of isopropanol is added. Next the loading gel is poured and a comb is placed to create the wells. After the loading gel
is polymerized the comb can be removed and the gel is ready for electrophoresis.
SDS-PAGE 3
Electrophoresis
First the anode and cathode buffers are prepared. The anode buffer usually contains Tris-Cl, distilled deionized water
and is adjusted to a higher pH than the cathode buffer. The cathode buffer contains SDS, Tris, Tricine, and distilled
deionized water. [7] [8]
The electrophoresis apparatus is set up with cathode buffer covering the gel in the negative electrode chamber, and
anode buffer in the lower positive electrode chamber. Next, the denatured sample proteins are added to the wells one
end of the gel with a syringe or pipette. Finally, the apparatus is hooked up to a power source under appropriate
running conditions to separate the protein bands.
An electric field is applied across the gel, causing the negatively-charged proteins to migrate across the gel towards
the positive (+) electrode (anode). Depending on their size, each protein will move differently through the gel matrix:
short proteins will more easily fit through the pores in the gel, while larger ones will have more difficulty (they
encounter more resistance). After a set amount of time (usually a few hours- though this depends on the voltage
applied across the gel; higher voltages run faster but tend to produce somewhat poorer resolution), the proteins will
have differentially migrated based on their size; smaller proteins will have traveled farther down the gel, while larger
ones will have remained closer to the point of origin. Therefore, proteins may be separated roughly according to size
(and therefore, molecular weight), certain glycoproteins behave anomalously on SDS gels.
SDS-PAGE 4
Staining
Following electrophoresis, the gel may be stained (most commonly
with Coomassie Brilliant Blue R-250 or silver stain), allowing
visualization of the separated proteins, or processed further (e.g.
Western blot). After staining, different proteins will appear as distinct
bands within the gel. It is common to run molecular markers of known
molecular weight in a separate lane in the gel, in order to calibrate the
gel and determine the weight of unknown proteins by comparing the
distance traveled relative to the marker. The gel is actually formed
because the acrylamide solution contains a small amount, generally
Two SDS-PAGE-gels after a completed run
about 1 part in 35 of bisacrylamide, which can form cross-links
between two polyacrylamide molecules. The ratio of acrylamide to
bisacrylamide can be varied for special purposes. The acrylamide concentration of the gel can also be varied,
generally in the range from 5% to 25%. Lower percentage gels are better for resolving very high molecular weight
proteins, while much higher percentages are needed to resolve smaller proteins. Determining how much of the
various solutions to mix together to make gels of particular acrylamide concentration can be done on line [9]
Gel electrophoresis is usually the first choice as an assay of protein purity due to its reliability and ease. The
presence of SDS and the denaturing step causes proteins to be separated solely based on size. False negatives and
positives are possible. A comigrating contaminant can appear as the same band as the desired protein. This
comigration could also cause a protein to run at a different position or to not be able to penetrate the gel. This is why
it is important to stain the entire gel including the stacking section. Coomassie Brilliant Blue will also bind with less
affinity to glycoproteins and fibrous proteins, which interferes with quantification.
Stacking gel
The stacking gel is a large pore PAG (4%T). This gel is
prepared with Tris/HCl buffer pH 6.8 of about 2 pH
units lower than that of electrophoresis buffer
(Tris/Glycine). These conditions provide an
environment for Kohlrausch reactions determining
molar conductivity, as a result, SDS-coated proteins are
concentrated to several fold and a thin starting zone of
the order of 19 μm is achieved in a few minutes. This
gel is cast over the resolving gel. The height of the
stacking gel region is always maintained more than
double the height and the volume of the sample to be
applied. This is based on isotachophoresis.
Chemical ingredients
• Tris (tris (hydroxy methyl) aminomethane)
(C4H11NO3; mW: 121.14). It has been used as a
buffer because it is an innocuous substance to most
proteins. Its pKa is 8.3 at 20 °C, making it a very
Transmission-Electron Microscopic image of a polyacrylamide gel.
satisfactory buffer in the pH range from roughly 7 to The pore size of a gel is determined by the total amount of monomer
9. present (%T) and the amount of cross-linker (%C).
structure. This is known as Native PAGE. Adding SDS solves this problem, as it binds to and unfolds the
protein, giving a near uniform negative charge along the length of the polypeptide.
• Ammonium persulfate (APS) (N2H8S2O8; mW: 228.2). APS is an initiator for gel formation.
• TEMED (N, N, N', N'-tetramethylethylenediamine) (C6H16N2; mW: 116.21). Chemical polymerisation of
acrylamide gel is used for SDS-PAGE. It can be initiated by ammonium persulfate and the quaternary amine,
N,N,N',N'-tetramethylethylenediamine (TEMED). The rate of polymerisation and the properties of the resulting
gel depends on the concentration of APS and TEMED. Increasing the amount of APS and TEMED results in a
decrease in the average polymer chain length, an increase in gel turbidity and a decrease in gel elasticity.
Decreasing the amount of initiators shows the reverse effect. The lowest catalytic concentrations that will allow
polymerisation in the optimal period of time should be used. APS and TEMED are used, approximately in
equimolar concentrations in the range of 1 to 10 mM.
Reducing SDS-PAGE
Besides the addition of SDS, proteins may optionally be briefly heated to near boiling in the presence of a reducing
agent, such as dithiothreitol (DTT) or traditionally 2-mercaptoethanol (beta-mercaptoethanol/BME), which further
denatures the proteins by reducing disulfide linkages, thus overcoming some forms of tertiary protein folding, and
breaking up quaternary protein structure (oligomeric subunits). This is known as reducing SDS-PAGE, and is most
commonly used. Non-reducing SDS-PAGE (no boiling and no reducing agent) may be used when native structure is
important in further analysis (e.g. enzyme activity, shown by the use of zymograms). For example, quantitative
preparative native continuous polyacrylamide gel electrophoresis (QPNC-PAGE) is a new method for separating
native metalloproteins in complex biological matrices.
SDS-PAGE 7
Silver staining
In the 14th century the silver staining technique was developed for colouring the
surface of glass. It has been used extensively for this purpose since the 16th
century. The colour produced by the early silver stains ranged between light yellow
and an orange-red. Camillo Golgi perfected the silver staining for the study of the
nervous system. Golgi's method stains a limited number of cells at random in their
entirety.[15] The exact chemical mechanism by which this happens is still largely
unknown.[16] Silver staining was introduced by Kerenyi and Gallyas as a sensitive
procedure to detect trace amounts of proteins in gels.[17] The technique has been
extended to the study of other biological macromolecules that have been separated
in a variety of supports.[18] Classical Coomassie Brilliant Blue staining can usually
detect a 50 ng protein band, Silver staining increases the sensitivity typically 50
times. Many variables can influence the colour intensity and every protein has its
own staining characteristics; clean glassware, pure reagents and water of highest
purity are the key points to successful staining.[19]
Buffer systems
Most protein separations are performed using a "discontinuous" buffer
system that significantly enhances the sharpness of the bands within
the gel. During electrophoresis in a discontinuous gel system, an ion
gradient is formed in the early stage of electrophoresis that causes all
of the proteins to focus into a single sharp band. This occurs in a region
of the gel that has larger pores so that the gel matrix does not retard the
migration during the focusing or "stacking" event. Negative ions from
the buffer in the tank then "outrun" the SDS-covered protein "stack"
and eliminate the ion gradient so that the proteins subsequently
separate by the sieving action in the lower, "resolving" region of the
gel.
pore gradient and the protein stack gradually disperses due to an frictional resistance increase of the gel matrix.
Stacking and unstacking occurs continuously in the gradient gel, for every protein at a different position. For a
complete protein unstacking the polyacrylamide-gel concentration must exceed 16% T. The two-gel system of
"Laemmli" is a simple gradient gel. The pH discontinuity of the buffers is of no significance for the separation
quality, and a "stacking-gel" with a different pH is not needed.
See also
• Capillary electrophoresis
• DNA electrophoresis
• Eastern blotting
• Electroblotting
• Electrophoresis
• Gel electrophoresis
• History of electrophoresis
• Isoelectric focusing
• Isotachophoresis
• Native Gel Electrophoresis
• Northern blotting
• Protein electrophoresis
• Southern blotting
• Two dimensional SDS-PAGE
• Western blotting
• Zymography
External links
• Demystifying SDS-PAGE Video [23]
• Demystifying SDS-PAGE [24]
• SDS-PAGE Calculator [25] for customised recipes for TRIS Urea gels.
• 2-Dimensional Protein Gelelectrophoresis [26]
• [27] Hempelmann E. SDS-Protein PAGE and Proteindetection by Silverstaining and Immunoblotting of
Plasmodium falciparum proteins. in: Moll K, Ljungström J, Perlmann H, Scherf A, Wahlgren M (eds) Methods in
Malaria Research, 5th edition, 2008, 263-266
References
[1] Shapiro AL, Viñuela E, Maizel JV Jr. (September 1967). "Molecular weight estimation of polypeptide chains by electrophoresis in
SDS-polyacrylamide gels.". Biochem Biophys Res Commun. 28 (5): 815–820. doi:10.1016/0006-291X(67)90391-9. PMID 4861258.
[2] Weber K, Osborn M (August 1969). "The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel
electrophoresis.". J Biol Chem. 244 (16): 4406–4412. PMID 5806584.
[3] Laemmli UK (August 1970). "Cleavage of structural proteins during the assembly of the head of bacteriophage T4". Nature 227 (5259):
680–685. doi:10.1038/227680a0. PMID 5432063.
[4] Caprette, David. "SDS-PAGE" (http:/ / www. ruf. rice. edu/ ~bioslabs/ studies/ sds-page/ denature. html). . Retrieved 27 Sept 2009.
[5] "What is the meaning of de -gas the acrylamide gel mix?" (http:/ / www. protocol-online. org/ biology-forums/ posts/ 17740. html). .
Retrieved 28 Sept 2009.
[6] "SDS-PAGE" (http:/ / www. science. smith. edu/ departments/ Biochem/ Biochem_353/ sdspage. html). . Retrieved 12 Sept 2009.
[7] Schägger, H; Von Jagow, G (1987). "Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the
range from 1 to 100 kDa.". Anal. Biochem. 166 (2): 368–379. doi:10.1016/0003-2697(87)90587-2. PMID 2449095.
[8] Andrews. "SDS-PAGE" (http:/ / www. dwalab. ca/ labman/ recipes/ PreparingtoRunTricineSDSGels. html). . Retrieved 27 Sept 2009.
[9] http:/ / encorbio. com/ protocols/ SDS-Calc. htm
SDS-PAGE 10
[10] Davis BJ, Ornstein L (1959). "A new high resolution electrophoresis method.". Delivered at the Society for the Study of Blood at the New
York Academy of Medicine.
[11] Raymond S, Weintraub L. (1959). "Acrylamide gel as a supporting medium for zone electrophoresis.". Science 130: 711.
doi:10.1126/science.130.3377.711. PMID 14436634.
[12] Rüchel R, Steere RL, Erbe EF (1978). "Transmission-electron microscopic observations of freeze-etched polyacrylamide gels.". J
Chromatogr. 166: 563–575. doi:10.1016/S0021-9673(00)95641-3.
[13] Ornstein L (December 1964). "DISC ELECTROPHORESIS. I. BACKGROUND AND THEORY.". Ann N Y Acad Sci. 121: 321–349.
doi:10.1111/j.1749-6632.1964.tb14207.x. PMID 14240533.
[14] Davis BJ (December 1964). "Disc Electrophoresis. 2, Method and application to human serum proteins". Ann. New York Acad. Sci 121:
404–427. doi:10.1111/j.1749-6632.1964.tb14213.x. PMID 14240539.
[15] Grant G (Oct 2007). "How the 1906 Nobel Prize in Physiology or Medicine was shared between Golgi and Cajal". Brain Res Rev 55 (2):
490–498. doi:10.1016/j.brainresrev.2006.11.004. PMID 17306375.
[16] Golgi C (1873). "Sulla struttura della sostanza grigia del cervello.". Gazzetta Medica Italiana (Lombardia) 33: 244–246.
[17] Kerenyi L, Gallyas F (1973). "Über Probleme der quantitiven Auswertung der mit physikalischer Entwicklung versilberten
Agarelektrophoretogramme". Clin. Chim. Acta 47 (3): 425–436. doi:10.1016/0009-8981(73)90276-3. PMID 4744834.
[18] Switzer RC 3rd, Merril CR, Shifrin S (Sep 1979). "A highly sensitive silver stain for detecting proteins and peptides in polyacrylamide
gels.". Anal Biochem. 98 (1): 231–237. doi:10.1016/0003-2697(79)90732-2. PMID 94518.
[19] Hempelmann E, Schulze M, Götze O (1984). "Free SH-groups are important for the polychromatic staining of proteins with silver nitrat".
Neuhof V (ed)Electrophoresis '84 , Verlag Chemie Weinheim 1984: 328–330.
[20] Schägger H, von Jagow G (1987). "Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the
range from 1 to 100 kDa.". Anal Biochem. 166 (2): 368–379. doi:10.1016/0003-2697(87)90587-2. PMID 2449095.
[21] Wiltfang J, Arold N, Neuhoff V (1991). "A new multiphasic buffer system for sodium dodecyl sulfate-polyacrylamide gel electrophoresis of
proteins and peptides with molecular masses 100,000-1000, and their detection with picomolar sensitivity.". Electrophoresis 12 (5): 352–366.
doi:10.1002/elps.1150120507. PMID 1718736.
[22] Kohlrausch F (1897). "Ueber Concentrations-Verschiebungen durch Electrolyse im Inneren von Lösungen und Lösungsgemischen.".
Ann.J.Phys.u.Chem. 62: 209–239. doi:10.1002/andp.18972981002.
[23] http:/ / sdspage. homestead. com/ TheVideo. html
[24] http:/ / sdspage. homestead. com/
[25] http:/ / www. omx-online. com/ calculator. html
[26] http:/ / wwwzb. zb. kfa-juelich. de/ wiki/ index. php?title=Sample_preparation_2D
[27] http:/ / www. biomalpar. org/ updatedMethods_In_Malaria_Research_5thedition. pdf
Article Sources and Contributors 11
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