Agarose gel electrophoresis is a method of
gel electrophoresis
Gel electrophoresis is a method for separation and analysis of biomacromolecules ( DNA, RNA, proteins, etc.) and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF ...
used in
biochemistry
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology and ...
,
molecular biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...
,
genetics
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar wor ...
, and
clinical chemistry
Clinical chemistry (also known as chemical pathology, clinical biochemistry or medical biochemistry) is the area of chemistry that is generally concerned with analysis of bodily fluids for diagnostic and therapeutic purposes. It is an applied ...
to separate a mixed population of macromolecules such as DNA or proteins in a matrix of
agarose
Agarose is a heteropolysaccharide, generally extracted from certain red seaweed. It is a linear polymer made up of the repeating unit of agarobiose, which is a disaccharide made up of D-galactose and 3,6-anhydro-L-galactopyranose. Agarose is o ...
, one of the two main components of
agar
Agar ( or ), or agar-agar, is a jelly-like substance consisting of polysaccharides obtained from the cell walls of some species of red algae, primarily from ogonori (''Gracilaria'') and "tengusa" (''Gelidiaceae''). As found in nature, agar is ...
. The proteins may be separated by charge and/or size (
isoelectric focusing
Isoelectric focusing (IEF), also known as electrofocusing, is a technique for separating different molecules by differences in their isoelectric point (pI). It is a type of zone electrophoresis usually performed on proteins in a gel that takes ad ...
agarose electrophoresis is essentially size independent), and the
DNA and
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 ...
fragments by length. Biomolecules are separated by applying an
electric field
An electric field (sometimes E-field) is the physical field that surrounds electrically charged particles and exerts force on all other charged particles in the field, either attracting or repelling them. It also refers to the physical field fo ...
to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix.
Agarose gel is easy to cast, has relatively fewer charged groups, and is particularly suitable for separating DNA of size range most often encountered in laboratories, which accounts for the popularity of its use. The separated DNA may be viewed with stain, most commonly under UV light, and the DNA fragments can be extracted from the gel with relative ease. Most agarose gels used are between 0.7–2% dissolved in a suitable electrophoresis buffer.
Properties of agarose gel
Agarose
Agarose is a heteropolysaccharide, generally extracted from certain red seaweed. It is a linear polymer made up of the repeating unit of agarobiose, which is a disaccharide made up of D-galactose and 3,6-anhydro-L-galactopyranose. Agarose is o ...
gel is a three-dimensional matrix formed of helical agarose molecules in supercoiled bundles that are aggregated into three-dimensional structures with channels and pores through which biomolecules can pass. The 3-D structure is held together with hydrogen bonds and can therefore be disrupted by heating back to a liquid state. The melting temperature is different from the gelling temperature, depending on the sources, agarose gel has a gelling temperature of 35–42 °C and a melting temperature of 85–95 °C. Low-melting and low-gelling agaroses made through chemical modifications are also available.
Agarose gel has large pore size and good gel strength, making it suitable as an anticonvection medium for the electrophoresis of DNA and large protein molecules. The pore size of a 1% gel has been estimated from 100 nm to 200–500 nm,
and its gel strength allows gels as dilute as 0.15% to form a slab for gel electrophoresis.
Low-concentration gels (0.1–0.2%) however are fragile and therefore hard to handle. Agarose gel has lower resolving power than polyacrylamide gel for DNA but has a greater range of separation, and is therefore used for DNA fragments of usually 50–20,000 bp in size. The limit of resolution for standard agarose gel electrophoresis is around 750 kb, but resolution of over 6 Mb is possible with
pulsed field gel electrophoresis
Pulsed field gel electrophoresis is a technique used for the separation of large DNA molecules by applying to a gel matrix an electric field that periodically changes direction.
Historical background
Standard gel electrophoresis techniques for s ...
(PFGE). It can also be used to separate large proteins, and it is the preferred matrix for the gel electrophoresis of particles with effective radii larger than 5–10 nm. A 0.9% agarose gel has pores large enough for the entry of
bacteriophage T4
Escherichia virus T4 is a species of bacteriophages that infect ''Escherichia coli'' bacteria. It is a double-stranded DNA virus in the subfamily '' Tevenvirinae'' from the family Myoviridae. T4 is capable of undergoing only a lytic lifecycle ...
.
The agarose polymer contains charged groups, in particular
pyruvate
Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell.
Pyruvic aci ...
and
sulphate
The sulfate or sulphate ion is a polyatomic anion with the empirical formula . Salts, acid derivatives, and peroxides of sulfate are widely used in industry. Sulfates occur widely in everyday life. Sulfates are salts of sulfuric acid and many ar ...
.
These negatively charged groups create a flow of water in the opposite direction to the movement of DNA in a process called
electroendosmosis Electroosmotic flow (or electro-osmotic flow, often abbreviated EOF; synonymous with electroosmosis or electroendosmosis) is the motion of liquid induced by an applied potential across a porous material, capillary tube, membrane, microchannel, or an ...
(EEO), and can therefore retard the movement of DNA and cause blurring of bands. Higher concentration gels would have higher electroendosmotic flow. Low EEO agarose is therefore generally preferred for use in agarose
gel electrophoresis of nucleic acids
Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules which are to be analyzed are set upon a viscous medium, the gel, where an electric field induces the nu ...
, but high EEO agarose may be used for other purposes. The lower sulphate content of low EEO agarose, particularly low-melting point (LMP) agarose, is also beneficial in cases where the DNA extracted from gel is to be used for further manipulation as the presence of contaminating sulphates may affect some subsequent procedures, such as
ligation
Ligation may refer to:
* Ligation (molecular biology), the covalent linking of two ends of DNA or RNA molecules
* In medicine, the making of a ligature (tie)
* Chemical ligation, the production of peptides from amino acids
* Tubal ligation, a meth ...
and
PCR. Zero EEO agaroses however are undesirable for some applications as they may be made by adding positively charged groups and such groups can affect subsequent enzyme reactions. Electroendosmosis is a reason agarose is used in preference to
agar
Agar ( or ), or agar-agar, is a jelly-like substance consisting of polysaccharides obtained from the cell walls of some species of red algae, primarily from ogonori (''Gracilaria'') and "tengusa" (''Gelidiaceae''). As found in nature, agar is ...
as the
agaropectin
Agaropectin is one of the two main components of agar and mainly consists of D-glucuronic acid and pyruvic acid.
Structure
Agaropectin is a sulphated galactan mixture which composes agar by 30% composition. It is the component of agar that is no ...
component in agar contains a significant amount of negatively charged sulphate and carboxyl groups. The removal of agaropectin in agarose substantially reduces the EEO, as well as reducing the non-specific adsorption of biomolecules to the gel matrix. However, for some applications such as the electrophoresis of serum proteins, a high EEO may be desirable, and agaropectin may be added in the gel used.
Migration of nucleic acids in agarose gel
Factors affecting migration of nucleic acid in gel
![Plasmid miniprep](https://upload.wikimedia.org/wikipedia/commons/2/2e/Plasmid_miniprep.jpg)
A number of factors can affect the migration of nucleic acids: the dimension of the gel pores (gel concentration), size of DNA being electrophoresed, the voltage used, the ionic strength of the buffer, and the concentration of intercalating dye such as ethidium bromide if used during electrophoresis.
Smaller molecules travel faster than larger molecules in gel, and double-stranded DNA moves at a rate that is inversely proportional to the logarithm of the number of base pairs. This relationship however breaks down with very large DNA fragments, and separation of very large DNA fragments requires the use of
pulsed field gel electrophoresis
Pulsed field gel electrophoresis is a technique used for the separation of large DNA molecules by applying to a gel matrix an electric field that periodically changes direction.
Historical background
Standard gel electrophoresis techniques for s ...
(PFGE), which applies alternating current from different directions and the large DNA fragments are separated as they reorient themselves with the changing field.
For standard agarose gel electrophoresis, larger molecules are resolved better using a low concentration gel while smaller molecules separate better at high concentration gel. Higher concentration gels, however, require longer run times (sometimes days).
The movement of the DNA may be affected by the
conformation of the DNA molecule, for example,
supercoiled DNA
DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. A given strand may be "positively supercoiled" or "negatively supercoiled" (more or less tightly wound). The amount of a st ...
usually moves faster than relaxed DNA because it is tightly coiled and hence more compact. In a normal plasmid DNA preparation, multiple forms of DNA may be present. Gel electrophoresis of the plasmids would normally show the negatively supercoiled form as the main band, while nicked DNA (open circular form) and the relaxed closed circular form appears as minor bands. The rate at which the various forms move however can change using different electrophoresis conditions,
and the mobility of larger circular DNA may be more strongly affected than linear DNA by the pore size of the gel.
Ethidium bromide which intercalates into circular DNA can change the charge, length, as well as the superhelicity of the DNA molecule, therefore its presence in gel during electrophoresis can affect its movement. For example, the positive charge of ethidium bromide can reduce the DNA movement by 15%.
Agarose gel electrophoresis can be used to resolve circular DNA with different supercoiling topology.
DNA damage due to increased
cross-link
In chemistry and biology a cross-link is a bond or a short sequence of bonds that links one polymer chain to another. These links may take the form of covalent bonds or ionic bonds and the polymers can be either synthetic polymers or natural ...
ing will also reduce electrophoretic DNA migration in a dose-dependent way.
The rate of migration of the DNA is proportional to the voltage applied, i.e. the higher the voltage, the faster the DNA moves. The resolution of large DNA fragments however is lower at high voltage. The mobility of DNA may also change in an unsteady field – in a field that is periodically reversed, the mobility of DNA of a particular size may drop significantly at a particular cycling frequency.
This phenomenon can result in band inversion in field inversion gel electrophoresis (FIGE), whereby larger DNA fragments move faster than smaller ones.
Migration anomalies
* "Smiley" gels - this edge effect is caused when the voltage applied is too high for the gel concentration used.
* Overloading of DNA - overloading of DNA slows down the migration of DNA fragments.
* Contamination - presence of impurities, such as salts or proteins can affect the movement of the DNA.
Mechanism of migration and separation
The negative charge of its phosphate backbone moves the DNA towards the positively charged anode during electrophoresis. However, the migration of DNA molecules in solution, in the absence of a gel matrix, is independent of molecular weight during electrophoresis.
The gel matrix is therefore responsible for the separation of DNA by size during electrophoresis, and a number of models exist to explain the mechanism of separation of biomolecules in gel matrix. A widely accepted one is the Ogston model which treats the polymer matrix as a sieve. A globular protein or a
random coil
In polymer chemistry, a random coil is a conformation of polymers where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the cha ...
DNA moves through the interconnected pores, and the movement of larger molecules is more likely to be impeded and slowed down by collisions with the gel matrix, and the molecules of different sizes can therefore be separated in this sieving process.
The Ogston model however breaks down for large molecules whereby the pores are significantly smaller than size of the molecule. For DNA molecules of size greater than 1 kb, a
reptation
A peculiarity of thermal motion of very long linear macromolecules in ''entangled'' polymer melts or concentrated polymer solutions is reptation. Derived from the word reptile, reptation suggests the movement of entangled polymer chains as bein ...
model (or its variants) is most commonly used. This model assumes that the DNA can crawl in a "snake-like" fashion (hence "reptation") through the pores as an elongated molecule. A biased reptation model applies at higher electric field strength, whereby the leading end of the molecule become strongly biased in the forward direction and pulls the rest of the molecule along.
Real-time fluorescence microscopy of stained molecules, however, showed more subtle dynamics during electrophoresis, with the DNA showing considerable elasticity as it alternately stretching in the direction of the applied field and then contracting into a ball, or becoming hooked into a U-shape when it gets caught on the polymer fibres.
General procedure
The details of an agarose gel electrophoresis experiment may vary depending on methods, but most follow a general procedure.
Casting of gel
The gel is prepared by dissolving the agarose powder in an appropriate buffer, such as
TAE or
TBE, to be used in electrophoresis.
The agarose is dispersed in the buffer before heating it to near-boiling point, but avoid boiling. The melted agarose is allowed to cool sufficiently before pouring the solution into a cast as the cast may warp or crack if the agarose solution is too hot. A comb is placed in the cast to create wells for loading sample, and the gel should be completely set before use.
The concentration of gel affects the resolution of DNA separation. The agarose gel is composed of microscopic pores through which the molecules travel, and there is an inverse relationship between the pore size of the agarose gel and the concentration – pore size decreases as the density of agarose fibers increases. High gel concentration improves separation of smaller DNA molecules, while lowering gel concentration permits large DNA molecules to be separated. The process allows fragments ranging from 50 base pairs to several mega bases to be separated depending on the gel concentration used. The concentration is measured in weight of agarose over volume of buffer used (g/ml). For a standard agarose gel electrophoresis, a 0.8% gel gives good separation or resolution of large 5–10kb DNA fragments, while 2% gel gives good resolution for small 0.2–1kb fragments. 1% gels is often used for a standard electrophoresis. High percentage gels are often brittle and may not set evenly, while low percentage gels (0.1-0.2%) are fragile and not easy to handle. Low-melting-point (LMP) agarose gels are also more fragile than normal agarose gel. Low-melting point agarose may be used on its own or simultaneously with standard agarose for the separation and isolation of DNA. PFGE and FIGE are often done with high percentage agarose gels.
Loading of samples
Once the gel has set, the comb is removed, leaving wells where DNA samples can be loaded. Loading buffer is mixed with the DNA sample before the mixture is loaded into the wells. The loading buffer contains a dense compound, which may be glycerol, sucrose, or
Ficoll
Ficoll is a neutral, highly branched, high-mass, hydrophilic polysaccharide which dissolves readily in aqueous solutions. Ficoll radii range from 2-7 nm. It is prepared by reaction of the polysaccharide with epichlorohydrin. Ficoll is a regi ...
, that raises the density of the sample so that the DNA sample may sink to the bottom of the well.
If the DNA sample contains residual ethanol after its preparation, it may float out of the well. The loading buffer also includes colored dyes such as
xylene cyanol
Xylene cyanol can be used as an electrophoretic color marker, or tracking dye, to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Bromophenol blue and orange G
Orange G also called C.I. 16230, Acid ...
and
bromophenol blue
Bromophenol blue (3′,3″,5′,5″-tetrabromophenolsulfonphthalein, BPB), albutest is used as a pH indicator, an electrophoretic color marker, and a dye. It can be prepared by slowly adding excess bromine to a hot solution of phenolsulfonpht ...
used to monitor the progress of the electrophoresis. The DNA samples are loaded using a
pipette
A pipette (sometimes spelled as pipett) is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. Pipettes come in several designs for various purposes with diffe ...
.
Electrophoresis
![Electrophoresis - Moving along gel](https://upload.wikimedia.org/wikipedia/commons/0/00/Electrophoresis_-_Moving_along_gel.jpg)
Agarose gel electrophoresis is most commonly done horizontally in a subaquaeous mode whereby the slab gel is completely submerged in buffer during electrophoresis. It is also possible, but less common, to perform the electrophoresis vertically, as well as horizontally with the gel raised on agarose legs using an appropriate apparatus. The buffer used in the gel is the same as the running buffer in the electrophoresis tank, which is why electrophoresis in the subaquaeous mode is possible with agarose gel.
For optimal resolution of DNA greater than 2kb in size in standard gel electrophoresis, 5 to 8 V/cm is recommended (the distance in cm refers to the distance between electrodes, therefore this recommended voltage would be 5 to 8 multiplied by the distance between the electrodes in cm).
[ Voltage may also be limited by the fact that it heats the gel and may cause the gel to melt if it is run at high voltage for a prolonged period, especially if the gel used is LMP agarose gel. Too high a voltage may also reduce resolution, as well as causing band streaking for large DNA molecules. Too low a voltage may lead to broadening of band for small DNA fragments due to dispersion and diffusion.
Since DNA is not visible in natural light, the progress of the electrophoresis is monitored using colored dyes. Xylene cyanol (light blue color) comigrates large DNA fragments, while Bromophenol blue (dark blue) comigrates with the smaller fragments. Less commonly used dyes include ]Cresol Red
Cresol red (full name: ''o''-cresolsulfonephthalein) is a triarylmethane dye frequently used for monitoring the pH in aquaria.
Molecular biology
Cresol red can be used in many common molecular biology reactions in place of other loading dyes. ...
and Orange G
Orange G also called C.I. 16230, Acid Orange 10, or orange gelb is a synthetic azo dye used in histology in many staining formulations. It usually comes as a disodium salt. It has the appearance of orange crystals or powder.
Staining
Orange G ...
which migrate ahead of bromophenol blue. A DNA marker A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be ...
is also run together for the estimation of the molecular weight of the DNA fragments. Note however that the size of a circular DNA like plasmids cannot be accurately gauged using standard markers unless it has been linearized by restriction digest
A restriction digest is a procedure used in molecular biology to prepare DNA for analysis or other processing. It is sometimes termed ''DNA fragmentation'' (this term is used for other procedures as well). Hartl and Jones describe it this way:
...
, alternatively a supercoiled DNA marker may be used.
Staining and visualization
DNA as well as RNA are normally visualized by staining with ethidium bromide
Ethidium bromide (or homidium bromide, chloride salt homidium chloride) is an intercalating agent commonly used as a fluorescent tag (nucleic acid stain) in molecular biology laboratories for techniques such as agarose gel electrophoresis. It i ...
, which intercalates into the major grooves of the DNA and fluoresces under UV light. The intercalation depends on the concentration of DNA and thus, a band with high intensity will indicate a higher amount of DNA compared to a band of less intensity. The ethidium bromide may be added to the agarose solution before it gels, or the DNA gel may be stained later after electrophoresis. Destaining of the gel is not necessary but may produce better images. Other methods of staining are available; examples are SYBR Green
SYBR Green I (SG) is an asymmetrical cyanine dye used as a nucleic acid stain in molecular biology. The SYBR family of dyes is produced by Molecular Probes Inc., now owned by Thermo Fisher Scientific. SYBR Green I binds to DNA. The resulting DN ...
, GelRed
GelRed is an intercalating nucleic acid stain used in molecular genetics for agarose gel DNA electrophoresis. GelRed structurally consists of two ethidium subunits that are bridged by a linear oxygenated spacer.
GelRed is a fluorophore, and its ...
, methylene blue
Methylthioninium chloride, commonly called methylene blue, is a salt used as a dye and as a medication. Methylene blue is a thiazine dye. As a medication, it is mainly used to treat methemoglobinemia by converting the ferric iron in hemoglobin ...
, brilliant cresyl blue
Brilliant cresyl blue is a supravital stain used for counting reticulocyte
Reticulocytes are immature red blood cells (RBCs). In the process of erythropoiesis (red blood cell formation), reticulocytes develop and mature in the bone marrow a ...
, Nile blue sulphate, and crystal violet
Crystal violet or gentian violet, also known as methyl violet 10B or hexamethyl pararosaniline chloride, is a triarylmethane dye used as a histological stain and in Gram's method of classifying bacteria. Crystal violet has antibacterial, antif ...
. SYBR Green, GelRed and other similar commercial products are sold as safer alternatives to ethidium bromide as it has been shown to be mutagenic
In genetics, a mutagen is a physical or chemical agent that permanently changes genetic material, usually DNA, in an organism and thus increases the frequency of mutations above the natural background level. As many mutations can cause cancer in ...
in Ames test, although the carcinogenicity
A carcinogen is any substance, radionuclide, or radiation that promotes carcinogenesis (the formation of cancer). This may be due to the ability to damage the genome or to the disruption of cellular metabolic processes. Several radioactive sub ...
of ethidium bromide has not actually been established. SYBR Green requires the use of a blue-light transilluminator. DNA stained with crystal violet can be viewed under natural light without the use of a UV transilluminator which is an advantage, however it may not produce a strong band.
When stained with ethidium bromide, the gel is viewed with an ultraviolet
Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nanometer, nm (with a corresponding frequency around 30 Hertz, PHz) to 400 nm (750 Hertz, THz), shorter than that of visible light, but longer than ...
(UV) transilluminator. The UV light excites the electrons within the aromatic ring of ethidium bromide, and once they return to the ground state, light is released, making the DNA and ethidium bromide complex fluoresce. Standard transilluminators use wavelengths of 302/312-nm (UV-B), however exposure of DNA to UV radiation for as little as 45 seconds can produce damage to DNA and affect subsequent procedures, for example reducing the efficiency of transformation
Transformation may refer to:
Science and mathematics
In biology and medicine
* Metamorphosis, the biological process of changing physical form after birth or hatching
* Malignant transformation, the process of cells becoming cancerous
* Trans ...
, ''in vitro'' transcription
Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including:
Genetics
* Transcription (biology), the copying of DNA into RNA, the fir ...
, and PCR. Exposure of DNA to UV radiation therefore should be limited. Using a higher wavelength of 365 nm (UV-A range) causes less damage to the DNA but also produces much weaker fluorescence with ethidium bromide. Where multiple wavelengths can be selected in the transilluminator, shorter wavelength can be used to capture images, while longer wavelength should be used if it is necessary to work on the gel for any extended period of time.
The transilluminator apparatus may also contain image capture devices, such as a digital or polaroid camera, that allow an image of the gel to be taken or printed.
For gel electrophoresis of protein, the bands may be visualised with Coomassie or silver stain In pathology, 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.
In traditional stained glass, silve ...
s.
Downstream procedures
The separated DNA bands are often used for further procedures, and a DNA band may be cut out of the gel as a slice, dissolved and purified. Contaminants however may affect some downstream procedures such as PCR, and low melting point agarose may be preferred in some cases as it contains fewer of the sulphates that can affect some enzymatic reactions. The gels may also be used for blotting techniques.
Buffers
In general, the ideal buffer should have good conductivity, produce less heat and have a long life. There are a number of buffers used for agarose electrophoresis; common ones for nucleic acids include Tris/Acetate/EDTA (TAE) and Tris/Borate/EDTA (TBE). The buffers used contain EDTA to inactivate many nucleases which require divalent cation for their function. The borate in TBE buffer can be problematic as borate can polymerize, and/or interact with cis diols such as those found in RNA. TAE has the lowest buffering capacity, but it provides the best resolution for larger DNA. This means a lower voltage and more time, but a better product.
Many other buffers have been proposed, e.g. lithium borate
Lithium borate, also known as lithium tetraborate is an inorganic compound with the formula Li2B4O7. A colorless solid, lithium borate is used in making glasses and ceramics.
Structure
Its structure consists of a polymeric borate backbone. The Li ...
(LB), iso electric histidine, pK matched goods buffers, etc.; in most cases the purported rationale is lower current (less heat) and or matched ion mobilities, which leads to longer buffer life. Tris-phosphate buffer has high buffering capacity but cannot be used if DNA extracted is to be used in phosphate sensitive reaction. LB is relatively new and is ineffective in resolving fragments larger than 5 kbp; However, with its low conductivity, a much higher voltage could be used (up to 35 V/cm), which means a shorter analysis time for routine electrophoresis. As low as one base pair size difference could be resolved in 3% agarose gel with an extremely low conductivity medium (1 mM lithium borate).
Other buffering system may be used in specific applications, for example, barbituric acid-sodium barbiturate or Tris-barbiturate
Barbiturates are a class of depressant drugs that are chemically derived from barbituric acid. They are effective when used medically as anxiolytics, hypnotics, and anticonvulsants, but have physical and psychological addiction potential as we ...
buffers may be used for in agarose gel electrophoresis of proteins, for example in the detection of abnormal distribution of proteins.
Applications
*Estimation of the size of DNA molecules following digestion with restriction enzyme
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...
s, e.g., in restriction map
A restriction map is a map of known restriction sites within a sequence of DNA. Restriction mapping requires the use of restriction enzymes. In molecular biology, restriction maps are used as a reference to engineer plasmids or other relatively ...
ping of cloned DNA.
*Estimation of the DNA concentration by comparing the intensity of the nucleic acid band with the corresponding band of the size marker.
*Analysis of products of a polymerase chain reaction
The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) t ...
(PCR), e.g., in molecular genetic diagnosis
Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, o ...
or genetic fingerprinting
DNA profiling (also called DNA fingerprinting) is the process of determining an individual's DNA characteristics. DNA analysis intended to identify a species, rather than an individual, is called DNA barcoding.
DNA profiling is a forensic tec ...
*Separation of DNA fragments for extraction and purification.
*Separation of restricted genomic DNA prior to Southern transfer, or of RNA prior to Northern transfer.
*Separation of proteins, for example, screening of protein abnormalities in clinical chemistry
Clinical chemistry (also known as chemical pathology, clinical biochemistry or medical biochemistry) is the area of chemistry that is generally concerned with analysis of bodily fluids for diagnostic and therapeutic purposes. It is an applied ...
.
Agarose gels are easily cast and handled compared to other matrices and nucleic acids are not chemically altered during electrophoresis. Samples are also easily recovered. After the experiment is finished, the resulting gel can be stored in a plastic bag in a refrigerator.
Electrophoresis is performed in buffer solutions to reduce pH changes due to the electric field, which is important because the charge of DNA and RNA depends on pH, but running for too long can exhaust the buffering capacity of the solution. Further, different preparations of genetic material may not migrate consistently with each other, for morphological or other reasons.
History
In the mid- to late 1960s, agarose and related gels were first found to be effective matrices for DNA and RNA electrophoresis.Nucleic Acid Gel Electrophoresis—A Brief Overview and History
ThermoFisher Scientific
See also
*
Gel electrophoresis
Gel electrophoresis is a method for separation and analysis of biomacromolecules ( DNA, RNA, proteins, etc.) and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF ...
*
Immunodiffusion
Immunodiffusion is a diagnostic test which involves diffusion through a substance such as agar which is generally soft gel agar (2%) or agarose (2%), used for the detection of antibodies or antigen.
The commonly known types are:
:# Single diffusi ...
,
Immunoelectrophoresis
Immunoelectrophoresis is a general name for a number of biochemical methods for separation and characterization of proteins based on electrophoresis and reaction with antibodies. All variants of immunoelectrophoresis require immunoglobulins, a ...
*
SDD-AGE
In biochemistry and molecular biology, SDD-AGE is short for Semi-Denaturating Detergent Agarose Gel Electrophoresis. This is a method for detecting and characterizing large protein polymers which are stable in 2% SDS at room temperature, unlike ...
*
Northern blot
The northern blot, or RNA blot,Gilbert, S. F. (2000) Developmental Biology, 6th Ed. Sunderland MA, Sinauer Associates. is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.K ...
*
SDS-polyacrylamide gel electrophoresis
*
Southern blot
A Southern blot is a method used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detecti ...
References
External links
How to run a DNA or RNA gelVideo and article of agarose gel electrophoresisA typical method from wikiversityBuilding a gel electrophoresis chamber
{{DEFAULTSORT:Agarose Gel Electrophoresis
Biological techniques and tools
Molecular biology
Electrophoresis
Polymerase chain reaction
Articles containing video clips