What is the main difference between protein electrophoresis and nucleic acid electrophoresis?

Answer 1

There are many similarities and differences between protein and DNA electrophoresis.

Similarities:

• PAGE protein and DNA electrophoresis both cause separation by size, creating bands that are viewed by the scientist or a machine. The smallest segments more the fastest due to less friction with the surface of their medium or equipment.
• The movement of charges through the medium is what causes the DNA or proteins to move. Electrons move from the negative to positive end of the gel or capillary tube.

Differences:

• In PAGE protein electrophoresis, a polyacrylamide gel is used to prevent convection from altering the movement of the proteins. If the proteins are charged, and there is a worry that the charge will affect the mobility of the protein segments, 1% SDS can be added to get rid of the mass/charge issue. This way, only the mass of the segment determines how far it moves. In DNA capillary electrophoresis, the size of the capillary is so small that it does not have room for convection to occur (it is only 20-50 microns wide). Thus, there is no medium in the capillary but DNA itself.
• In protein electrophoresis, the proteins are often dyed so their movement can be viewed with the naked eye, or a machine. With DNA capillary electrophoresis, DNA strands are made through DNA replication with dNTPs that are fluorescently labeled for the different nucleotides. Each base is labeled a different color. A fine laser lights up the DNA strand in the capillary tube and reads what color fluoresces. This is how the nucleotide is identified.
• Protein PAGE electrophoresis is used to determine the purity of a protein sample. It can also be used to see how large the chains are that make up a multi-chain protein if a denaturing agent is added. DNA electrophoresis is used to get the order of nucleotides in a DNA sequence. It is done by chopping the DNA sequence into many smaller bits and sequencing them, then putting them back together by lining them up according to sequence overlaps. This is called the "shotgun" method. Protein electrophoresis can figure out the order of about 15-20 amino acids by a similar method, but DNA electrophoresis can get up to 1000 nucleotides (~300 amino acids). DNA electrophoresis is limited by the low probability that the DNA sequence would be cut into a segment greater than 1000 nucleotides.

Answer 2

The meaning of electrophoresis is the same in both cases. Either nucleic acids or proteins, this technique separate the molecules according to their charges. However there are some differences based upon the nature of the molecules. Two major differences in the technique are:

a) Nucleic acids electrophoresis is done mainly in agarose gels, while protein electrophoresis is carried out in different materials, the most common is polyacrylamide.

b) After protein electrophoresis, developing of protein bands in the gel is acquired by immersing it in different stain solutions, the most commons are Coomassie brilliant blue, and Amido black. On the other hand, to develop the nucleic acid bands on the agarose gels, it is necessary to use a specific dye that fluoresces under UV light, that is, the ethidium bromide dye.