Week 2 Lab: DNA Gel Art

Image 1 (Mid-run photograph): The photograph taken during electrophoresis shows the gel submerged in TAE within the gel box. Two colored dye fronts are faintly visible — a blue band and a dark purple band — but they appear localized to only one or two lanes. The majority of the gel appears empty, with no visible dye migration in the other wells. This is already an early indicator that most wells were either not loaded successfully or contained insufficient DNA.

Image 2 (GeneSnap image): The final imaging result is largely dark. Only a single lane shows any detectable fluorescence — a faint, somewhat smeared signal concentrated in what appears to be one lane, with no clearly resolved discrete bands. The remaining lanes are entirely blank. This represents an unsuccessful gel run in terms of the intended gel art pattern.

Analysis of What Went Wrong Based on the observations made during lab sessions and the photographic evidence, several compounding factors likely contributed to the result:

1. Pipetting error during well loading. When I was loading the fourth slot, the pipette tip was not properly inserted into the well. This is a critical failure point. In submerged gel electrophoresis, the wells are filled with buffer. The loading dye’s density causes the sample to sink — but only if it is dispensed directly into the well. If the tip hovers above the well or is positioned outside it, the sample disperses into the surrounding buffer and is effectively lost. This likely explains why most lanes are empty on the final image.
2. Insufficient electrophoresis run time due to electrical issues. There was an unforeseen electrical short circuit that cut the run time short. This is consistent with the imaging result — even in the one lane that has signal, the DNA has not migrated very far, and there is no clear band resolution. A truncated run means fragments have not separated sufficiently, resulting in a compressed, smeared appearance rather than discrete bands. The faint dye fronts visible in Image 1 also suggest limited migration distance.
3. Potential variability in reaction preparation. Another plausible explanation adding to the result could be the differences in mixing or component proportions across the PCR tubes. This is plausible as if the Lambda DNA stock was not thoroughly vortexed or flicked, concentration could vary between tubes. Similarly, enzyme or buffer pipetting errors at the 1–3 μL scale are common and can result in incomplete digestion or no digestion at all, though the imaging suggests the bigger problem was DNA not being present in the wells at all.
4. Low overall signal intensity. Even the one visible lane is quite faint. This could indicate that the total DNA mass loaded was below the detection threshold of SYBR Safe under blue light excitation. With 1.5 μg of Lambda DNA per reaction and SYBR Safe staining, bands should normally be clearly visible. The faintness suggests either DNA was lost during loading, the stain was not adequately mixed into the gel, or the transilluminator exposure settings were suboptimal.