<P> 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 . 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 . </P> <P> There are limits to electrophoretic techniques . Since passing current through a gel causes heating, gels may melt during electrophoresis . 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 . There are also limitations in determining the molecular weight by SDS - PAGE, especially if you are trying to find the MW of an unknown protein . There are certain biological variables that are difficult or impossible to minimize and can affect the electrophoretic migration . Such factors include protein structure, post-translational modifications, and amino acid composition . For example, tropomyosin is an acidic protein that migrates abnormally on SDS - PAGE gels . This is because the acidic residues are repelled by the negatively charged SDS, leading to an inaccurate mass - to - charge ratio and migration . Further, different preparations of genetic material may not migrate consistently with each other, for morphological or other reasons . </P> <P> The types of gel most typically used are agarose and polyacrylamide gels . Each type of gel is well - suited to different types and sizes of analyte . Polyacrylamide gels are usually used for proteins, and have very high resolving power for small fragments of DNA (5 - 500 bp). Agarose gels on the other hand have lower resolving power for DNA but have greater range of separation, and are therefore used for DNA fragments of usually 50 - 20,000 bp in size, but resolution of over 6 Mb is possible with pulsed field gel electrophoresis (PFGE). Polyacrylamide gels are run in a vertical configuration while agarose gels are typically run horizontally in a submarine mode . They also differ in their casting methodology, as agarose sets thermally, while polyacrylamide forms in a chemical polymerization reaction . </P> <P> Agarose gels are made from the natural polysaccharide polymers extracted from seaweed . Agarose gels are easily cast and handled compared to other matrices, because the gel setting is a physical rather than chemical change . Samples are also easily recovered . After the experiment is finished, the resulting gel can be stored in a plastic bag in a refrigerator . </P>

What is the difference between agarose gel and polyacrylamide gel electrophoresis
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