= PCR verification with gel electrophoresis
Biology experiments are hard, and so they go wrong, a lot.
For this reason, it is wise to verify that certain steps are correct whenever possible.
And so this is the first thing we did on the second day!
<Gel electrophoresis> separates molecules by their charge-to-mass ratio. It is one of those ultra common lab procedures!
This allows us to determine how long are the DNA fragments present in our solution.
Since we know that we amplified the 16S regions which we know the rough size of (there might be a bit of variability across species, but not that much), we were expecting to see a big band at that size.
And that is exactly what we saw!
First we had to prepare the gel, put the gel comb, and pipette the samples into wells present in the gel:
\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Gel_electrophoresis_insert_comb.jpg/360px-Gel_electrophoresis_insert_comb.jpg]
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\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Gel_electrophoresis_top_view_with_wells_visible.jpg/360px-Gel_electrophoresis_top_view_with_wells_visible.jpg]
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\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/a/a7/Gel_electrophoresis_pipette_sample_into_wells.jpg/360px-Gel_electrophoresis_pipette_sample_into_wells.jpg]
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To see the DNA, we added <ethidium bromide> to the samples, which is a substance that that both binds to DNA and is fluorescent.
Because it interacts heavily with DNA, ethidium bromide is a <mutagen>, and the biology people sure did treat the dedicated electrophoresis bench area with respect! <image Gel electrophoresis dedicated bench area to prevent ethidium bromide contamination.>{full}.
\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Gel_electrophoresis_dedicated_bench_area_to_prevent_ethidium_bromide_contamination.jpg/360px-Gel_electrophoresis_dedicated_bench_area_to_prevent_ethidium_bromide_contamination.jpg]
{title=<Gel electrophoresis> dedicated bench area to prevent <ethidium bromide> contamination.}
\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Gel_electrophoresis_dedicated_waste_bin_for_centrifuge_tubes_and_pipette_tips_contaminated_with_ethidium_bromide.jpg/360px-Gel_electrophoresis_dedicated_waste_bin_for_centrifuge_tubes_and_pipette_tips_contaminated_with_ethidium_bromide.jpg]
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The UV transilluminator we used to shoot <UV light> into the gel was the <Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator>. The fluorescent substance then emitted a light we can see.
As barely seen at <image Fischer Scientific UVP LM-26E Benchtop 2UV Transilluminator illuminated gel.>{full} due to bad photo quality due to lack of light, there is one strong green line, which compared to the ladder matches our expected 16S length. What we saw it with the naked eyes was very clear however.
\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/0/06/Fischer_Scientific_UVP_LM-26E_Benchtop_2UV_Transilluminator.jpg/640px-Fischer_Scientific_UVP_LM-26E_Benchtop_2UV_Transilluminator.jpg]
{title=Fischer Scientific UVP LM-26E Benchtop 2UV Transilluminator}
\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/8/85/Fischer_Scientific_UVP_LM-26E_Benchtop_2UV_Transilluminator_loading_gel.jpg/360px-Fischer_Scientific_UVP_LM-26E_Benchtop_2UV_Transilluminator_loading_gel.jpg]
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\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Fischer_Scientific_UVP_LM-26E_Benchtop_2UV_Transilluminator_illuminated_gel.jpg/360px-Fischer_Scientific_UVP_LM-26E_Benchtop_2UV_Transilluminator_illuminated_gel.jpg]
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