Imagine that you collected your data above, threw away the gel, and re-ran PCR again on the same samples, but using a different set of primers. How will the 2nd gel differ from the first since you're using a different set of primers?
When running PCR, the choice of primers is crucial as they determine the specific DNA sequences that will be amplified. If you use a different set of primers in the second PCR run, it will likely produce a different set of amplified DNA fragments compared to the first run.
To understand how the second gel will differ, we need to consider the differences between the two sets of primers. Primers are short DNA sequences that are designed to bind to specific regions on the DNA template. They serve as the starting point for DNA amplification during PCR. If the primers used in the second PCR run are designed to target different regions of the DNA compared to the primers used in the first run, this will result in the amplification of different DNA fragments.
Here are a few possible scenarios:
1. Different fragment sizes: If the primers used in the second PCR run are designed to bind to regions of the DNA template that are further apart or closer together compared to the first primers, the resulting DNA fragments will have different sizes. This will be reflected in the gel as distinct bands at different positions.
2. Absence of specific fragments: If the second set of primers does not target the same regions as the first set, certain specific DNA fragments amplified in the first run may not be amplified in the second run. Consequently, these fragments will not appear on the second gel.
3. Appearance of new fragments: Conversely, the second set of primers may target regions that were not amplified in the first run. This could result in the generation of new DNA fragments that were not present in the first gel.
In summary, using a different set of primers in the second PCR run will likely produce a different set of amplified DNA fragments, leading to differences in the resulting gel image. The specific variations will depend on the design and targeting of the new primers compared to the initial set used.