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.