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Agarose is purified from agar, a gelatinous substance isolated from seaweed. Different purities of agarose are commercially available as are agaroses with different melting properties. Agarose forms pores ranging from 100 nm to 300 nm in diameter depending upon the concentration of agarose used in the gel.
Small nucleic acids are better separated by polyacrylamide gels, large DNA molecules are only able to move end-on and are more difficult to separate.
Buffers
There are a number of buffers used for agarose electrophoresis. The most common being: Tris Acetate EDTA (TAE), Tris Borate EDTA (TBE) and Sodium Borate (SB). TAE has the lowest buffering capacity but provides good resolution for larger DNA gels have to be run at a lower voltage for a longer time. SB is relatively ineffective in resolving fragments larger than 5 kbp; however, with its low conductivity, a much higher voltage can be used, which means a shorter analysis time. TBE provides adequate buffering and good resolution and is most commonly used.
Visualization
The most common dye used for agarose gel electrophoresis is ethidium bromide, abbreviated as EtBr. The ethidium bromide intercalates between the DNA bases and fluoresces reddish-orange under ultraviolet light. By running DNA through an EtBr-treated gel and visualizing it with UV light, distinct bands of DNA become visible.
Agarose gel with samples loaded in the slots, before the electrophoresis process
The electrophoretic mobility or distance traveled by a DNA fragment during electrophoresis is inversely proportional to the logarithm of its size (usually given as base pairs or kilobase pairs) The migration distance of a DNA fragment in question can be compared with a plot of the distances migrated by a set of standard nucleic acid fragments to determine its size.
In the given plot; a) How far will a 0.5 kb DNA fragment travel? b) What is the size of a fragment which has migrated 16 mm?
The relationship between the log of a DNAs size and its electrophoretic mobility deviates strongly from linearity if the DNA is very large.
In standard agarose gel electrophoresis, it is difficult to separate molecules more than 50 kb as longer molecules run as a single slowly migrating band. To separate them, orthogonal field alternation gel electrophoresis (OFAGE) is used. The electric field alternates between two pairs of electrodes each positioned at an angle of 45 to the length of the gel. DNA molecules still move down the gel but each change in the field forces the molecules to realign. Shorter molecules realign more quickly than longer ones and so migrate more rapidly through the gel. OFAGE enables molecules upto 2 Mb in length to be separated.
4) dNTPs: The concentration of each dNTP in the reaction mixture is usually 200 M. It is very important to have equal concentrations of each dNTP (dATP, dCTP, dGTP, dTTP), as inaccuracy in the concentration of even a single dNTP dramatically increases the misincorporation level. When maximum fidelity of the PCR process is crucial, the final dNTP concentration should be 10-50 M, since the fidelity of DNA synthesis is maximal in this concentration range. 5) Taq DNA Polymerase: Usually 1-1.5 u of Taq DNA Polymerase are used in 50 l of reaction mix. Higher Taq DNA Polymerase concentrations may cause synthesis of nonspecific products. However, if inhibitors are present in the reaction mix (e.g., if the template DNA used is not highly purified), higher amounts of Taq DNA Polymerase (2-3 u) may be necessary.
Cycling Conditions
Initial Denaturation Step. The complete denaturation of the DNA template at the start of the PCR reaction is of importance. Incomplete denaturation of DNA results in the inefficient utilization of template in the first amplification cycle and in a poor yield of PCR product. The initial denaturation should be performed over an interval of 1-3 min at 95C if the GC content is 50% or less. This interval should be extended up to 10 min for GC-rich templates. If the initial denaturation is no longer than 3 min at 95C, Taq DNA Polymerase can be added into the initial reaction mixture. Denaturation Step. Usually denaturation for 0.5-2 min at 94-95C is sufficient, since the PCR product synthesized in the first amplification cycle is significantly shorter than the template DNA and is completely denatured under these conditions. Primer Annealing Step. Usually the optimal annealing temperature is 5C lower than the melting temperature of primer-template DNA duplex. Incubation for 0.5-2 min is usually sufficient. However, if nonspecific PCR products are obtained in addition to the expected product, the annealing temperature should be optimized by increasing it stepwise by 12C.
Extending Step. Usually the extending step is performed at 70-75C. The rate of DNA synthesis by Taq DNA Polymerase is highest at this temperature. Recommended extending time is 1 min for the synthesis of PCR fragments up to 2 kb. When larger DNA fragments are amplified, the extending time is usually increased by 1 min for each 1000 bp. Number of Cycles. The number of PCR cycles depends on the amount of template DNA in the reaction mix and on the expected yield of the PCR product. For less than 10 copies of template DNA, 40 cycles should be performed. If the initial quantity of template DNA is higher, 25-35 cycles are usually sufficient. Final Extending Step. After the last cycle, the samples are usually incubated at 72C for 5-15 min to fill-in the protruding ends of newly synthesized PCR products. Also, during this step, the terminal transferase activity of Taq DNA Polymerase adds extra A nucleotides to the 3'-ends of PCR products. If PCR fragments are to be cloned into T/A vectors, this step can be prolonged up to 30 min.
Applications of PCR
1) PCR allows isolation of DNA fragments from genomic DNA by selective amplification of a specific region of DNA. This use of PCR augments many methods, such as Southern and Northern blotting and DNA cloning, that require large amounts of DNA, representing a specific DNA region. PCR supplies these techniques with high amounts of pure DNA, enabling analysis of DNA samples even from very small amounts of starting material. 2) PCR can also be used for the isolation of a DNA sequence for recombinant DNA technologies involving the insertion of a DNA sequence into a plasmid or the genetic material of another organism. 3) PCR may also be used for genetic fingerprinting, a forensic technique used to identify a person or organism by comparing experimental DNAs. As PCR amplifies the regions of DNA that it targets, PCR can be used to analyze extremely small amounts of sample. This is often critical for forensic analysis, when only a trace amount of DNA is available as evidence. A variation of this technique can also be used to determine evolutionary relationships among organisms. Thus, PCR may also be used in the analysis of ancient DNA that is thousands of years old. .
4) In analysis of diseases. Viral DNA can be detected by PCR. The primers used need to be specific to the targeted sequences in the DNA of a virus, and the PCR can be used for diagnostic analyses or DNA sequencing of the viral genome. The high sensitivity of PCR permits virus detection soon after infection and even before the onset of disease. 5) Quantitative PCR methods allow the estimation of the amount of a given sequence present in a sample a technique often applied to quantitatively determine levels of gene expression. Real-time PCR is an established tool for DNA quantification that measures the accumulation of DNA product after each round of PCR amplification
DNA sequencing