Discussion

In the lab experiment performed, DNA was isolated from cheek cells and run through a Polymerase Chain Reaction (PCR) in order to amplify the Alu insertion gene. Gel electrophoresis was then used to separate out the isolated DNA into specific banding patterns in order to determine if the gene was present. The results of our groups gel are indicated in the picture taken by the UV transilluminator. Clearly the most notable feature in the photograph is the specific banding pattern established by the Molecular Weight Marker (MWM). The purpose of the marker is both to serve as a control and to provide a legend for interpreting the approximate number of base pairs at each band. The fact that the MWM turned out so clearly indicates that the gel electrophoresis procedure worked correctly. In addition a blank well with just loading dye was added into well number 5 as a control and its results indicate that of no other contamination in the gel that might affect the samples run. Banding patterns could only be obtained for one member of our group, that of a Mr. Keith Elliott. In reference to the MWM , Mr. Elliott exhibited a clear and distinct band at the 400bp marker indicating that he in fact may have an Alu insertion on locus b, his genotype thus being b+. Mr. Elliott also exhibited another band beyond that of the 100bp marker (along with another member of our group). Subsequent discussion with the professor about such patterns lead us to discount the validity of these bands. It is likely that the bands may be part of a non targeted gene sequence lying adjacent to the Alu insertion that was mistakenly targeted and amplified through PCR. No banding patterns were exhibited for the rest of the group members. The reasons for this may include an error in proper loading of gel wells as well as a procedural error in preparing and running the gel electrophoresis, however this idea seems highly unlikely given the remarkable clarity of the MWM bands as well as the banding pattern obtained for Mr. Elliott. The most likely reason for the lack of a banding pattern obtained must lie in a procedural error in preparing the PCR mix. Given the instability of both the primer and enzyme mixes, it is entirely possible that the mixes were degraded to a point of ineffectiveness by not keeping them properly stored on ice during the preparation. As to which specific mix was ineffective or the molecular basis of degradation there is no clear way to tell without re-testing the solutions against a fresh set of control mixes. However, the results of degradation in either solution would have the same net effect during the PCR reaction, that of no duplication of the Alu insertion sequence. Additional controls that could be run might include two sets of MWMs on the two end wells in order to establish a uniform banding pattern and check the current and gel for consistency. Running the electrophoresis directly after PCR activity might also reduce the likelihood of losing isolated DNA in vitro that has been frozen, stored and thawed.