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A mixture of fragmented DNA was electrophoresed in an agarose gel. After staining the gel with ethidium bromide, no DNA bands were observed. What could be the reason?

Last updated date: 20th Jun 2024
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Hint: Gel electrophoresis is a method to separate mixtures of DNA, RNA, or proteins based on their molecular size.

Complete Answer:
Gel electrophoresis is used for the separation of DNA fragments for DNA fingerprinting, to examine the results of Polymerase chain reaction, to examine genes related to a particular disease.
In this method, an electrical field is created which pushes the molecules (to be separated) with the help of a gel that contains small pores. By this method, a small DNA molecule travels a greater distance via gel as compared to larger DNA molecules.

After staining the gel with ethidium bromide, if no DNA bands were observed, then this may occur due to any of the following reasons-
i) If the mixture becomes contaminated with enzymes like nucleases.
ii) If the concentration of gel is not adequate.
iii) The cathode and anode are kept in the opposite orientation.
In general, DNA is negatively charged and moves towards a positive electrode, i.e., the anode. The lower bottom side is positively charged.
iv) Inadequate concentration of ethidium bromide which is required to be intercalated within the DNA bases.

Note: Ethidium bromide (EtBr) is mostly used for detecting DNA/RNA. EtBr acts as an intercalation of DNA which inserts itself into the spaces between the base pairs of double-helix DNA. EtBr is also used during the process of DNA fragment separation by agarose gel electrophoresis. It is also used to reduce mitochondrial DNA copy number in growing cells. It acts as a mutagen.