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Two-dimensional electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. The basic idea is to separate proteins contained in a sample using two independent properties such isoelectric point and mass. In the gel, each spot represents a protein accumulation and its size depends on the amount of protein present in the sample.

One of the reasons of the popularity of 2D gel electrophoresis is its simplicity. As a counterpart, the experimental setting and the materials used do not allow a highly controlled experiment. This means that strong variations between corresponding sets of spots are expected. To compare samples, we need to process several images in a single experiment. For this kind of diferential analysis DIGE experiments are carried out. Difference gel electrophoresis where up to three different protein samples can be labeled with fluorescent dyes (for example Cy3, Cy5, Cy2) prior to two-dimensional electrophoresis.

Electrophoresis: Basics and types
Description of DIGE technique
Another descriptive article about DIGE: Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Unlu M, Morgan ME, Minden JS. Electrophoresis. 1997 Oct;18(11):2071-7


Source: www.mosbio.eu