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Gel Electrophoresis

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Learn about Gel Electrophoresis

 

Gel Electrophoresis

This Gel Electrophoresis site is your portal for all things related to the gel electrophoresis technique and its analysis. Here we provide you with all the background information, protocols, analysis steps, visualization and troubleshooting information for separating DNA, RNA or Protein on gels to become the ultimate expert in gel electrophoresis!

Gel Electrophoresis Table of Contents

 

What is Gel Electrophoresis?

Gel electrophoresis is a method used in molecular biology to separate biological samples.

Gel Electrophoresis employs a gel matrix to separate molecules usually by size and/or charge.

Matrices include Agarose for DNA or RNA, and Polyacrilamide for Proteins.

Agarose Gels

Agarose gels are usually run for DNA or Protein separations. Agarose is extracted from seaweed, and is a biological polymer which is easily cast into gels.

The biological agarose polymers are heated first and then cooled into a matrix capable of separating molecules.

For agarose gel casting slabs in the shape of a square or rectangle are used.

The agarose gel contains pores through which molecules can be drawn like a sieve through. The size of the pores is a property of the concentration of agarose used when creating the gel. Using a comb before the agarose hardens, lanes or wells for loading samples for separation such as DNA are formed at one end of the gel.

 

agarose gel electrophoresis

 

Types of Gel Electrophoresis

Applications of Gel Electrophoresis

Gel electrophoresis is used in analysis or separation of DNA, RNA or protein molecules.

 Thus gel electrophoresis allows:

  1. Separation of restriction enzyme digested DNA including genomic DNA, prior to Southern Blot transfer. It is also often used for separating RNA prior to Northern transfer.
  2. Analysis of PCR products after polymerase chain reaction to assess for target DNA amplification.
  3. Allows for the estimation of the size of DNA molecules using a DNA marker or ladder which contains DNA fragments of various known sizes.
  4. Allows the rough estimation of DNA quantity and quality.
  5. Quantity is assessed using lambda DNA ladder which contains specific amounts of DNA in different bands.
  6. Quality of DNA is assessed by observing the absence of streaking or fragments (or contaminating DNA bands).
  7. Other techniques rely on agarose gel electrophoresis for DNA separation including DNA fingerprinting.

Advantages and Disadvantages of Gel Electrophoresis

The advantages are that the gel is easily poured, does not denature the samples. The samples can also be recovered.

The disadvantages are that gels can melt during electrophoresis, the buffer can become exhausted, and different forms of genetic material may run in unpredictable forms.