Gel electrophoresis

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Gel electrophoresis

Gel electrophoresis apparatus – An agarose gel is

placed in this buffer-filled box and electrical field is
applied via the power supply to the rear. The negative
terminal is at the far end (black wire), so DNA
migrates toward the camera.
Classification Electrophoresis
Other techniques
Capillary electrophoresis
SDS-PAGE
Two-dimensional gel
Related
electrophoresis
Temperature gradient gel
electrophoresis

Gel electrophoresis refers to using a gel as an anticonvective medium and or seiving medium
during electrophoresis. Gel electrophresis is most commonly used for separation of biological
macromolecules such as deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or protein;
however, gel electrophoresis can be used for separation of nanoparticles. Electrophoresis refers
to 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 seiving 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.[1] DNA Gel electrophoresis is usually performed for
analytical purposes, often after amplification of DNA via 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.
Contents
[hide]

 1 Separation
 2 Visualization
 3 Applications
o 3.1 Nucleic acids
o 3.2 Proteins
 4 History
 5 See also
 6 References
 7 External links

[edit] Separation
In simple terms: Electrophoresis is a procedure which enables the sorting of molecules based on
size and charge. Using an electric field, molecules (such as DNA) can be made to move through
a gel made of agar. The molecules being sorted are dispensed into a well in the gel material. The
gel is placed in an electrophoresis chamber, which is then connected to a power source. When
the electric current is applied, the larger molecules move more slowly through the gel while the
smaller molecules move faster. The different sized molecules form distinct bands on the gel.
[citation needed]

The term "gel" in this instance refers to the matrix used to contain, then separate the target
molecules. In most cases, the gel is a crosslinked polymer whose composition and porosity is
chosen based on the specific weight and composition of the target to be analyzed. When
separating proteins or small nucleic acids (DNA, RNA, or oligonucleotides) the gel is usually
composed of different concentrations of acrylamide and a cross-linker, producing different sized
mesh networks of polyacrylamide. When separating larger nucleic acids (greater than a few
hundred bases), the preferred matrix is purified agarose. In both cases, the gel forms a solid, yet
porous matrix. Acrylamide, in contrast to polyacrylamide, is a neurotoxin and must be handled
using appropriate safety precautions to avoid poisoning. Agarose is composed of long
unbranched chains of uncharged carbohydrate without cross links resulting in a gel with large
pores allowing for the separation of macromolecules and macromolecular complexes.[citation needed]

"Electrophoresis" refers to the electromotive force (EMF) that is used to move the molecules
through the gel matrix. By placing the molecules in wells in the gel and applying an electric
field, the molecules will move through the matrix at different rates, determined largely by their
mass when the charge to mass ratio (Z) of all species is uniform, toward the anode if negatively
charged or toward the cathode if positively charged.[2]

[edit] Visualization
Gel electrophoresis

After the electrophoresis is complete, the molecules in the gel can be stained to make them
visible. Ethidium bromide, silver, or Coomassie Brilliant Blue dye may be used for this process.
Other methods may also be used to visualize the separation of the mixture's components on the
gel. If the analyte molecules fluoresce under ultraviolet light, a photograph can be taken of the
gel under ultraviolet lighting conditions, often using a Gel Doc. If the molecules to be separated
contain radioactivity added for visibility, an autoradiogram can be recorded of the gel.[citation needed]

If several samples have been loaded into adjacent wells in the gel, they will run parallel in
individual lanes. Depending on the number of different molecules, each lane shows separation of
the components from the original mixture as one or more distinct bands, one band per
component. Incomplete separation of the components can lead to overlapping bands, or to
indistinguishable smears representing multiple unresolved components.[citation needed]

Bands in different lanes that end up at the same distance from the top contain molecules that
passed through the gel with the same speed, which usually means they are approximately the
same size. There are molecular weight size markers available that contain a mixture of molecules
of known sizes. If such a marker was run on one lane in the gel parallel to the unknown samples,
the bands observed can be compared to those of the unknown in order to determine their size.
The distance a band travels is approximately inversely proportional to the logarithm of the size
of the molecule.[citation needed]

[edit] Applications
Gel electrophoresis is used in forensics, molecular biology, genetics, microbiology and
biochemistry. The results can be analyzed quantitatively by visualizing the gel with UV light and
a gel imaging device. The image is recorded with a computer operated camera, and the intensity
of the band or spot of interest is measured and compared against standard or markers loaded on
the same gel. The measurement and analysis are mostly done with specialized software.

Depending on the type of analysis being performed, other techniques are often implemented in
conjunction with the results of gel electrophoresis, providing a wide range of field-specific
applications.
[edit] Nucleic acids

An agarose gel of a PCR product compared to a DNA ladder.

In the case of nucleic acids, the direction of migration, from negative to positive electrodes, is
due to the naturally-occurring negative charge carried by their sugar-phosphate backbone.[3]

Double-stranded DNA fragments naturally behave as long rods, so their migration through the
gel is relative to their size or, for cyclic fragments, their radius of gyration. Single-stranded DNA
or RNA tend to fold up into molecules with complex shapes and migrate through the gel in a
complicated manner based on their tertiary structure. Therefore, agents that disrupt the hydrogen
bonds, such as sodium hydroxide or formamide, are used to denature the nucleic acids and cause
them to behave as long rods again.[4]

Gel electrophoresis of large DNA or RNA is usually done by agarose gel electrophoresis. See the
"Chain termination method" page for an example of a polyacrylamide DNA sequencing gel.
Characterization through ligand interaction of nucleic acids or fragments may be performed by
mobility shift affinity electrophoresis.

Electrophoresis of RNA samples can be used to check for genomic DNA contamination and also
for RNA degradation. RNA from eukaryotic organisms shows distinct bands of 28s and 18s
rRNA, the 28s band being approximately twice as intense as the 18s band. Degraded RNA has
less sharpely defined bands, has a smeared appearance, and intensity ratio is less than 2:1.

[edit] Proteins
SDS-PAGE autoradiography – The indicated proteins are present in different concentrations in
the two samples.

Proteins, unlike nucleic acids, can have varying charges and complex shapes, therefore they may
not migrate into the polyacrylamide gel at similar rates, or at all, when placing a negative to
positive EMF on the sample. Proteins therefore, are usually denatured in the presence of a
detergent such as sodium dodecyl sulfate/sodium dodecyl phosphate (SDS/SDP) that coats the
proteins with a negative charge.[1] Generally, the amount of SDS bound is relative to the size of
the protein (usually 1.4g SDS per gram of protein), so that the resulting denatured proteins have
an overall negative charge, and all the proteins have a similar charge to mass ratio. Since
denatured proteins act like long rods instead of having a complex tertiary shape, the rate at which
the resulting SDS coated proteins migrate in the gel is relative only to its size and not its charge
or shape.[1]

Proteins are usually analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis
(SDS-PAGE), by native gel electrophoresis, by quantitative preparative native continuous
polyacrylamide gel electrophoresis (QPNC-PAGE), or by 2-D electrophoresis.

Characterization through ligand interaction may be performed by electroblotting or by affinity

electrophoresis in agarose or by capillary electrophoresis as for estimation of binding constants
and determination of structural features like glycan content through lectin binding.