Jerome was running a DNA gel. Once the bromophenol blue dye reached about 2/3 down the gel, he unplugged the box, took out the gel and immediately placed it under UV light. He turned on the light but there were no visible bands on the gel and even the ladder lane looked completely empty. What do you think is the MOST likely explanation for this result?

Question

BlackTom AI · Accepted Answer

Start by restating the scenario to anchor the analysis: Jerome ran a DNA gel, unplugged when the dye had only partially migrated, and upon UV illumination neither the gel nor the ladder lane showed any bands. Now, evaluate each possible explanation in turn.
Option 1: 'He forgot to stain the gel with DNA binding dye which will fluorescence under UV light and make the DNA bands visible.' If the gel was not stained with a DNA-binding dye, the DNA would not fluoresce under UV, so no bands would be visible. This explanation directly accounts for the complete lack of visible bands, including the ladder, because both samples and ladder rely on the dye to be detected under UV illumination.
Option 2: 'He did not run the gel for long enough.' Short runs can produce faint or small bands, but the ladder (a defined DNA size marker) should still appear as bands even after a relatively short run, provided staining and illumination are correct. Moreover, if the dye and dye-front were functioning, at least some bands would typically be detectable. The absence of all bands suggests a problem with visualization rather than just insufficient separation time.
Option 3: 'He ran the gel for too long and all the DNA pieces ran off the gel making the gel completely empty.' In capillary terms this could happen for very large fragments, but in standard agarose gels the DNA bands remain within the gel unless the run is extreme or the gel is run into the buffer reservoir; usually the ladder would still show bands unless visualization failed. If the dye and gel were properly prepared, you would expect to see something unless the dye was missing or other visualization issues occurred. This option is less consistent with a completely empty gel under UV.
Option 4: 'He forgot to stain the gel with DNA binding dye which will fluorescence under UV light and make the DNA bands visible.' This is identical in meaning to Option 1 and should be treated as a duplicate stem-wise. Reiterating this point helps ensure we recognize that the core issue is the absence of a fluorescent stain required for detection under UV light.
In summary, the most coherent explanation that aligns with the observed lack of bands in both the sample lanes and the ladder is the lack of a DNA-binding stain, which would render all DNA molecules non-fluorescent under UV and thus invisible on the gel.

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