DESKTOP ELECTROPHORESIS LAB - MOVING
is a technique used for the separation of molecules by means of
electric current. In this case, the molecules to be separated
are placed in wells of an agarose gel medium which is submerged
below the surface of a buffer. The molecules will move in the
electrical field according to their charges. The positively charged
molecules will move to the negative electrode (cathode) and the
negatively charged molecules will move to the positive electrode
TARGET ABILITY LEVEL:
Regular, Honors or A.P. Biology
To build efficient electrophoresis systems for less than $15.00
each and use them to demonstrate electrophoretic ability of stain
molecules and materials such as DNA.Th
One day to build the boxes and power sources if each class takes
up where the previous class left off. One class period to pour
gels and one class period to load and run the gels (based on 55
minute class periods).
MATERIALS FOR BUILDING ELECTROPHORESIS
- #10 or 11 Rubbermaid Container
- 18 gauge (or so) seizing wire
(purchased at local boat shop)
- Microscope plastic slide box (lid or bottom)
- Hot glue/hot glue gun
- Dissecting Needle
- Aquarium Sealant
- 5 nine-volt batteries
- 1 nine-volt battery clip (cut in half)
- 2 alligator clips (1 black/1 red)
- Electrical or masking tape
Although 45 volts do not deliver enough current to be harmful
to the human body, students should be instructed not to place
fingers in the buffer solution and to close the containers while
current is running. Use appropriate precautions in use of electrical
gun, hot glue, and pointed objects.
Also, please refer to the appropriate
MSDS sheets for the stains/dyes used.
PROCEDURE FOR BUILDING BOXES AND
- Secure one portion of the microscope
slide box in the bottom of the Rubbermaid container with aquarium
sealant, flat side up and open side down (using the lid requires
less buffer). To produce a good seal, place sealant on all four
edges of the slide box, place in appropriate position and press.
- Using a dissecting needle, make
2 holes through the wall of one side of the container just above
the upper rim, and at least 1 cm to either side of the slide box
platform. This orientation will be referred to as the front
side of the box.
- Cut two pieces of wire about 4 cm
longer than the width of the Rubbermaid container. Bend the end
of the wire at a 90 degree angle where it touches the inside of
the back side of the container. Mold the remainder of the wire
so that the portion beyond the 90 degree bend runs toward the
front of the box parallel to and approximately 0.5 cm to 1 cm
above the floor of the container. Bend the wire at another 90
degree angle where it touches the inside of the front wall and
another 90 degrees out to the outside of the box via the hole
punched with the dissecting needle.
- Secure the wire at the original
90 degree bend to the back wall of the container with ample hot
glue to prevent separation. Also seal around the wire where it
emerges through the hole to the outside. ALLOW BOX TO DRY 24
HOURS, THEN CHECK FOR LEAKS.
- Bend the wires that stick out of
the holes into loops for attachment of alligator clip leads from
the power pack.
- To Make the Power Pack, arrange
the 5 nine-volt batteries as shown in above figure. Carefully separate
the wires of the nine-volt battery clip and snip with scissors
into + and - leads. Attach the wires to the appropriate alligator
clips (black to - and red to +) and secure by covering with plastic
lever covers which are part of the original clips.
PART II: MOVING MOLECULES
LAB (Addie Jackson) WL
- 2 X 3 in. glass microscope slide
Index card and thick cardboard cut to fit glass slide (to build up slide to fit comb)
3 X 5 index card
Pi-pump (Pipetor) to fit 10 ml pipet
10 ml Pipet
Agarose gel (liquid, slightly warmer than room temperature)
Electrophoresis chambers & power supplies built in Part I
Micropipet plungers and micropipets
- Tris EDTA Borate Buffer, pH 8.2 or 8.6.
Stains: Any stains available to you may be used.
POURING THE GEL:
- Place a clean glass slide onto an
index card and cut it to fit the glass slide.
- Fasten clips to both ends of the
comb and align the comb in the middle of the slide so that the
teeth of the comb just touch the glass. If teeth do not
touch, build the slide up using as many pieces of cardboard as
necessary. (see above figure - Equipment page)
- Carefully remove the white card
underneath leaving a small space between the teeth of the comb
and the surface of the glass slide. This insures a stable floor
for each well.
- Using the pi-pump, aspirate 9 ml
of warm (not hot) liquid agar into a pipet.
- Holding the pipet tip at a slight
angle, release the agarose slowly but continuously on the surface
of the glass slide, beginning around the teeth of the comb
and working toward the edges of the slide, filling in as you proceed.
The agarose will be held around the edges of the slide by surface
tension if the agarose is carefully applied and is not forced
over the edges. Try to avoid bubbles in the gel.
- Allow the gel to cool until it appears
opaque; then pull up on one side of the comb, applying continuous
but gentle pressure.
- The gel should remain on the slide
throughout the electrophoresis. If the gel is not going to be
used immediately, place it in a Zip-loc bag, blow in a small amount
of air to cushion it, then zip it shut securely. The gels can
then be stacked without damage and refrigerated until time for
- Place the gel on the platform in
the electrophoresis chamber and pour the buffer over it until
the gel is completely submerged. (See above figure - Electrophoresis
LOADING THE GEL:
- Insert the metal plunger into the
glass capillary tube micropipet See above figure - Electrophoresis Equipment
diagrams) and aspirate 10 microliters of a dye sample into the
pipet. Wipe the tip with a Kimwipe to remove excess.
- Carefully insert the tip of the
micropipetor above and into the corner of a well. Depress the
plunger slowly and carefully, filling the entire well. Continue
for each well, using the plunger designated for each stain/dye.
- As you place each sample into its
separate well, label a clean white index card, designating the
stain in each well.
RUNNING THE GEL:
- Close the lid of the electrophoresis
- Attach leads (alligator clips) to
wires on box and clip to power supply.
- Label the index card with positive
(+) (red) and negative (-) (black) poles in relation to stains
in the wells. Caution: Use homemade 45-volt power supplies
with homemade boxes to prevent shock hazard. Do NOT use variable
power supplies on which power can be cranked up to unsafe levels.
- Do not touch chamber or place fingers
in buffer once power has been turned on.
- Allow the gel to run for 10 minutes.
Disconnect the power. Remove the lid and observe the movement
of the stains.
- Replace the lid and reattach the
leads. Continue the electrophoresis until the fastest moving
dye comes to within 1 cm of the end of the gel, or 30 minutes.
Be sure to replace the correct lead to each wire as before:
red to positive and black to negative.
- Turn off the power and remove the
gel from the electrophoresis chamber. Using a spatula, place
the gel on an index card. Label the stains.
- Measure the distance each stain
migrated from the origin (well). Record the data in a table.
- Which molecules were negatively
- Which molecules were positively
- What factors, other than charge,
could have influenced the movement of these molecules?
- If an unknown was used, determine
which stains were in the mixture, and give the supporting evidence
from your data.
SOURCES FOR EQUIPMENT AND SUPPLIES
Modern Biology, Inc.
P.O. Box 97
Dayton, IN 47941-0097
E-C Apparatus Corp
3831 Tyrone Blvd. North
St. Petersburg, FL 33709
1530 Lindbergh Drive
P.O. Box 752
Beaumont, TX 77704
Sigma Chemical Corp.
P.O. Box 14508
St. Louis, MO 63178
PREPARATION OF TRIS EDTA BUFFER
SOLUTION: pH 8.2 - 8.6
Dissolve buffer crystals in distilled
water as per instructions provided by vendor.
(Modern Biology buffer uses one 60
g package in water to produce 3000 ml of solution)
PREPARATION OF AGAROSE GEL:
- Dissolve 10 grams of agarose gel
powder in 100 ml freshly prepared buffer solution.
- Heat the agarose-buffer mixture
in a boiling water bath on a hot plate until the agarose is clear
and boils gently for 2 minutes. Remove from hot plate and allow
to cool only until container is comfortable to touch. At this
point students should pour their gels.
Stains may sometimes be less dense
than the buffer solution. Hence, they will float to the surface
rather than sink into the wells when applied. To check, place
small amounts of buffer in small test tubes. Carefully apply
a drop of the stain to the surface of the buffer solution. If
the stain sinks, the stain is dense enough. If the stain disperses
over the surface of the buffer, add a few drops of 1:1 glycerin:buffer
solution. Reliable students may do this for you while you are
Methylene Blue, Methyl Green, Poncean Red, Safranin, Crystal Violet,
Comassie Blue, Bromphenol Blue, Dye or Stain Mixture*, etc.
*Dye or Stain Mixture is suggested
for comparison and identification of unknowns.
- Do not allow agarose gel to cool
too long prior to use as it will begin to set up in the flask
and will not pour smoothly.
- Distribute liquid agarose gel to
students in 100 ml units contained in 250 ml flasks to facilitate
pouring several gels at one time.
- Remind students to empty pipets
while gel is still warm or it will set up in pipet.
- Prepare buffer a day in advance
and keep under refrigeration. Gels run best with cold buffer.
- Pour buffer into gel chambers for
students, to avoid excessive use on their part.
- For first time electrophoresis,
Modern Biology sends everything prepackaged and provides excellent
information/instructions for both teacher and student.
- BE SURE TO CHECK LOCAL LEGAL GUIDELINES OF YOUR SCHOOL DISTRICT
FOR USE OF HOMEMADE ELECTRICAL APPARATUS IN THE CLASSROOM, IF
ANY. Under NO circumstances should a commercial variable powersource
be used on which power can be cranked up to unsafe levels.
Westwood High School
12400 Mellow Meadow Dr.
Austin, TX 78750