Question

Which gel, the genomic DNA or the PCR products would you add ethidium bromide to, and which gel would you stain in an ethidium bromide bath? Explain why you would make these choices?

Answer 1

Ethidium bromide (EtBr) is used to visualize both genomic DNA and PCR products in agarose gel electrophoresis. Genomic DNA is commonly mixed with EtBr before electrophoresis, while PCR products are typically stained in an EtBr bath after electrophoresis due to their abundance and to reduce background noise.

Step-by-step explanation:

In the context of agarose gel electrophoresis, both genomic DNA and PCR products can be visualized using ethidium bromide (EtBr) staining. Ethidium bromide inserts into the DNA and, when the gel is exposed to UV light, the DNA 'lights up' due to fluorescence. For genomic DNA, which is usually visualized after restriction enzyme digestion, it is common to add ethidium bromide directly to the agarose gel before electrophoresis. On the other hand, PCR products, which are often abundant, can be stained after electrophoresis by placing the gel in an ethidium bromide bath.

One would choose to add ethidium bromide to the gel containing genomic DNA to visualize the fragments as a smear, which can later be used for techniques like Southern blotting. For PCR products, staining post-electrophoresis in an EtBr bath ensures that the abundant PCR-amplified DNA is visible under fluorescent illumination without background noise that might obscure the bands of interest.