Limitations
 
Electrophoresis units have an upper limit in the voltage they can tolerate before heating up the gel, depending on their ability to dissipate heat. This phenomenon can be understood through the following equation:
P= I2R
where the power (P) produced by the system measured in watts is proportional to the resistance times the square of the current. Voltage tolerated by a gel before starting to heat up will depend on the amount of power (heat) that can be dissipated by the apparatus.

Regarding electrophoresis of proteins, this technique only detects variation in aminoacids that results in differences in the net charge of the proteins (only one third of aminoacids substitutions). Also, not all enzymes can be stained with the available staining protocols. With respect to DNA electrophoresis, bands can only be visualized when there is a certain amount of DNA (arround 30 ng); so when DNA amounts are small, they should be amplified by PCR (Polymerase Change Reaction).

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