Tag: agarose gel electrophoresis

Percent Agarose Gel

Agarose concentration in a gel is expressed in percentage of agarose to the volume of the buffer (w/v). For example,…

Tips to Reduce Run-time of Agarose Gel Electrophoresis

Usually agarose gel electrophoresis is performed at constant low voltage (5 – 10 V/cm). High voltage results in excessive heat…

Protocol: Visualizing DNA Bands in Agarose Gel Using GelRed – Precast Method

GelRed is a DNA staining dye and can be used to visualize DNA embedded in agarose gel. Both precast (GelRed…

Applications of Agarose Gel Electrophoresis

Agarose gel electrophoresis is extensively used for the analysis of nucleic acid. Observations made by running DNA or RNA samples on agarose gel are very helpful to determine quantity and quality of nucleic acids. These powerful features make agarose gel electrophoresis an important essential step in many well known techniques such as northern and southern blotting, RFLP, RAPD, PCR, molecular cloning etc. Since agarose gel allows the elution of biomolecules, it can also be used for the purification of nucleic acids and large protein molecules and complexes. In addition, it can also be used to analyse biological processes such as apoptosis.

Migration of Bromophenol Blue and Xylene Cyanol in Agarose Gel Running in TBE or TAE Electrophoresis Buffer

Bromophenol blue and Xylene cyanol are the two most commonly used tracking dyes for the analysis of DNA on agarose gel electrophoresis. These negatively charged dyes not only help in monitoring the progress of agarose gel electrophoresis but also allow easy monitoring of sample loading process onto the wells of agarose gel. Their position in relation to DNA fragments is an important information that helps to determine how far a gel must be run without accidentally letting the DNA fragments of interest run out of the gel and at the same time ensuring good resolution among different size DNA fragments.

Protocol: Running DNA Samples in Agarose Gel

Agarose gel is placed in an electrophoresis tank filled with an electrophoresis buffer. DNA samples are mixed with DNA loading dye and loaded onto the wells of agarose gel. Electrophoresis apparatus is connected to electric supply and electrophoresis is performed at constant voltage until the desired separation among DNA fragments is achieved. After the run is over, gel is analyzed using UV-transilluminator or Gel Doc system.

Agarose Gel Preparation Process

Preparation of Agarose Gel for DNA Analysis

Agarose Gel is a gelatin-like slab, which contains small wells for loading DNA samples. It is prepared by melting agarose in a suitable electrophoresis buffer. Molten agarose is then poured into a specialized tray (casting tray), which controls the size and shape of the gel. The comb is used to create wells in agarose gel.