Gel Electrophoresis and DNA
Extraction Lab
Spencer Cody
7-12 Hoven Science
Purpose:
The purpose of the gel electrophoresis lab was to
give students experience in using gel
electrophoresis, increase understanding in how
DNA technology is used, improve upon DNA
extraction skills from a prior lab, be able to
successfully mimic a fingerprint for multiple fruits
and vegetables, and to be able to successfully
test alternatives to gel electrophoresis that utilize
materials in place of EDTA buffer.
Standards:
This lab procedure covers the following South
Dakota state standards:
SD: 9-12.S.1.1
9-12.S.1.2
9-12.L.2.2
DNA Extraction:
1. Cut up and mash
sample fruit or
vegetable using a
mortar and pestle.
2. Once the sample is
thoroughly mashed,
transfer your sample
into a 300 mL beaker.
3. Add 50 mL of water
to your mashed sample,
one teaspoon of
shampoo, and 1 gram
of salt.
DNA Extraction:
4. Use a glass stirring
rod to carefully mix the
mashed contents, water,
salt, and shampoo
without generating
bubbles.
5. After mixing the
mashed mixture for two
minutes, transfer the
mixture into a filter
flask apparatus. Make
sure that the mashed
material is not seeping
through folds in your
filter paper.
Four different samples were used:
squash, potato, apple, and pear.
DNA Extraction:
6. Once all filtrate is
collected in the filter
flask, use a pipette to
transfer the filtrate to a
test tube.
7. Add 3 mL of cold
ethanol to the test tube.
Allow the ethanol and
filtrate to sit for five
minutes allowing for the
DNA to precipitate out
of solution.
Aspirators make filtration much
faster.
DNA Extraction:
8. Transfer the white
precipitated DNA to a
crucible using a pipette.
9. Add one drop of
methylene blue to the
precipitated DNA.
10. Add approximately
50% more volume to
the DNA sample using
glycerol.
10. Transfer to a well.
Methylene blue will supposedly bind
to DNA much like ethidium bromide.
Gel Run:
1. Add 0.4 grams of
agarose to 40 mL of
EDTA buffer.
2. Heat until EDTA
buffer completely
dissolves all the
agarose.
3. Pour the solution
into the gel mold with
comb in place.
4. Allow to cool.
EDTA buffer gel compared to a
sodium borate gel.
Gel Run:
5. Connect 9-volt
batteries in a series or
any other batteries you
can find.
6. Run gels for at least
an hour.
7. View and compare
the genomic
fingerprints.
Approximately 40 volts in series on
two gel electrophoresis machines.
Loading the gel:
Students loaded their
gels with four samples:
squash, pear, apple, and
potato DNA.
The elongated pipette
and glycerol makes
loading the gel possible.
Excess methylene blue will quickly
collect on the positive terminal.
Results:
Students loaded their
gels with four samples:
squash, pear, apple, and
potato DNA.
The elongated pipette
and glycerol makes
loading the gel possible.
Sodium borate gel was
extremely difficult to
load…supersaturated
solution precipitate?
Genomic fingerprints after running
for one hour.
Results:
Students were able to successfully extract and
precipitate DNA from several fruit and vegetable
samples. Students’ understanding of gel
electrophoresis increased along with their
understanding of DNA technology. Students
were not, however, able to produce reliable
fingerprints nor were they able to compare
among the fingerprints of the different fruits and
vegetables.
Future Improvements:
*Determine what variables may allow a direct
comparison among different genomes using this
procedure.
*Determine which alternative buffer works best
for this procedure.
*Determine how to make this lab more user
friendly for students.