How important in investigating DNA fragment the water content?
When removing the combs from the matrices to create the wells for the DNA sample, the agarose gel produced ones that were clean and uniform. Whereas, none of the strawberry jelly concentrations was able to achieve wells identical to the ones the agarose gel had. Although the quality of the wells in the strawberry jelly, in comparison to the agarose, did increase with viscosity, only the matrix with 10% of the water content was able to achieve wells that were most similar to the ones in the agarose gel.
Within the first 60 minutes of running the strawberry gels, the effervescence, starting at the carbon fibre tissue and developing through the gel, was more pronounced than in the agarose gel. Once the running time had been completed, and the stain applied, the DNA fragments were more visible and prominent in the agarose gel rather than in any of the strawberry jelly concentrations. In contrast, the DNA fragments appeared thicker in the strawberry jelly than they did in the agarose gel, albeit less clear. Furthermore, the separation of fragments in the agarose gel produced DNA fragments which were more uniform in size and shape. Not one of the strawberry jelly matrices was able to resolve multiple, distinct bands of DNA; only a single plasmid was produced. Thus, a run of the agarose gel and strawberry jelly matrices, containing just a single plasmid, was conducted for comparison and analysis.
The value for the third run of the 75% jelly was not included in the calculation for the mean distance as a result was interpreted as anomalous. A reason for this result may be due to excess evaporation during the running of the gel. If the comb was not placed properly over the gel tank or if it was dislodged, more evaporation may have occurred thereby reducing the water content in the matrix even further. Following my hypothesis, lesser water content may result in a reduction in pore size thus restricting the movement of the DNA fragment.
From the numerical data collected and the side-by-side comparison of the gel slabs, we observe that increasing the viscosity reduces the movement capacity of the DNA fragments. However, it can be noted that each viscosity did still produce the single band of DNA.
Interestingly, there is little difference in movement between the 25% and 50% concentrations, perhaps due to contamination, or possibly due to there being little change in pore size in line with the change around those particular concentrations. On the other hand, the overall trend in movement of the DNA fragments would suggest that, similarly to agarose as reported by Neves and Reis, increasing the strawberry jelly concentration (i.e. decreasing water content) decreases the pore size, and hence hinders the migration of the fragments.