gel electrophoresis chamber

ELECTROPHORESIS CHAMBER

Constructing your own Plexiglas® electrophoresis chamber is quite easy, inexpensive and fun. After you have made your chamber, try it out using the Colorful Electrophoresis experiments.

SAFETY: Remember to wear safety glasses at all times while constructing this chamber.

TIP: Leave the paper on each Plexiglas piece until you are ready to use it. Write the name of each piece of Plexiglas® on the paper covering the surface before beginning construction. Remove the paper as you work with each piece.


Bonding Plexiglas® pieces together

Bonding pieces of Plexiglas together is most easily accomplished with two people working together. One person holds the pieces in position, and the other person uses a syringe or Pasteur pipette to apply a thin line of acrylic bonding agent along both sides of the seam where the two pieces of Plexiglas meet. The liquid should wick between the two pieces of Plexiglas at the seam and bond them together within 2 minutes (hold them firmly together until bonded). It is very important to hold the pieces together firmly while bonding so that a leak-proof seal is made.

If a mistake is made in gluing pieces together and you discover it before the bond has fully set, the pieces can be snapped apart and re-bonded.
gel carrier

Pieces will bond best if you hold them so that the seam is horizontal. It is also better to hold the pieces so that the seam is not close to the table/surface you are working on. This allows any excess liquid to evaporate quickly. If the seam is close to or on a table/surface, the liquid may wick underneath and smear the Plexiglas.


Step 6
A. Construct the Gel Carrier

1. You will need the following pieces of Plexiglas:
* Gel Carrier Base - 3-3/4" by 3-3/4" by 3/4" thick
* Gel Carrier Sides (2) - 3-3/4" by 1/2" by 1/2" thick
2. Cut a slot 3/16" from one end of each Gel Carrier Side. The slots should be 1/16" wide x 1/8" deep; the Teflon® should fit easily into the slots. If desired, cut a second slot 1-5/8" from the first slot. gel carrier side view
3. Remove the paper from the Gel Carrier Sides and the Gel Carrier Base.
4. Lay the Gel Carrier Base on a flat surface. Lay the Gel Carrier Sides on top, on opposite edges, along the sides.
TIP: Make sure that the slots in the Gel Carrier Sides line up.
5. Turn the Gel Carrier Base on its edge, and bond the top Gel Carrier Side to it. Turning the Gel Carrier Base on its edge while bonding prevents the bonding agent from flowing underneath and smearing the Plexiglas.
6. Turn the Gel Carrier Base on the other edge, and bond the other Gel Carrier Side to it.

Step 5

Step 8
B. Cut the Gel Comb

1. You will need the 3-5/8" by 1" by 1/16" thick Teflon piece.
2. Copy the comb pattern onto paper or paperboard and cut it out.
3. Place the pattern in the gel carrier slots and check to make sure that the bottom edges of the comb teeth will be at least 1/16" (2 mm) above the Gel Carrier Base. It is very important that the wells in the gel formed by the teeth not go all of the way through the gel. Modify the pattern if needed.
4. Use a permanent marker to trace the pattern on the Teflon or tape the pattern down on the Teflon.
5. Place the Teflon on a piece of scrap lumber or cardboard and cut out the comb using an X-acto (TM) knife.
6. Use fine sandpaper (150 grit) to smooth the edges of the Comb teeth so that they will not rip the wells in the gel when the Comb is removed.
7. Place the comb in the slots in the Gel Carrier sides. If it does not slide in and out of the slots easily, sand the flat surface of the Teflon so that it does slide easily.
8. Again place the comb in the slots in the Gel Carrier sides. Check that the bottom edge of each comb tooth is at least 2mm (1/16") above the Gel Carrier Base. If any are not, sand them down.



comb pattern (click on image for printing instructions)
Step 7

Step 7

Step 10
C. Drill holes for the leads to the power supply

1. You will need the following pieces of Plexiglas:
* Chamber Long Side - one of the 7-1/2" by 2-1/2" by 1/4" thick pieces
* Chamber Lid Front - 7-1/2" by 1-1/4" by 1/4" thick

TIP: Do not remove the paper from these pieces until you are ready to bond them together

drilling holes
2. Lay the Chamber Lid Front on top of the Chamber Long Side, matching the two pieces along one long edge and the two sides. Tape the two sides together with masking tape so that the pieces do not slip while drilling.
3. Mark "X's" on the top edges and "X's" on the paper of the sides facing you. This will assist you in bonding the pieces together in the correct orientation later.
4. On the Chamber Lid Front, measure in 1" from each short end and make a pencil mark. Measure down 5/8" from one long edge and make cross marks in the centers of the first marks; you should have a "+" mark at each end of the Lid Front.
5. Place the point of a nail at the center of each "+" mark and tap the head of the nail with a hammer to make a guide hole for the drill bit.
6. If you are using an electric hand drill, place the Plexiglas pieces on top of a piece of scrap lumber. Place a C-clamp in the center of the long edges of the Plexiglas and clamp the Plexiglas/wood sandwich onto a table top in preparation for drilling.
7. Use a 9/64" drill bit to drill holes through both pieces of Plexiglas® in the places you made the guide holes (in the center of the "+" marks).
TIP: Use a small brush to lightly oil the bit before drilling. This will help keep the Plexiglas® from bonding to the bit as it heats up during drilling.
8. Unclamp the Plexiglas and remove the masking tape holding the two pieces together.

Chamber Lid Front
9. Clamp the Chamber Lid Front down for drilling with the side opposite the "X" up. Remember the piece of scrap lumber if you are using an electric hand drill.
10. Use the 5/16" bit to drill through the entire thickness of the Lid Front, centering the tip of the drill in the 9/64" holes
TIP: Remember to lightly oil the bit before drilling.
11. Unclamp the Lid Front.

Step 4
D. Construct the Chamber Lid

1. You will need the following pieces of Plexiglas:
* Chamber Lid Front - 7-1/2" by 1-1/4" by 1/4" thick piece with holes drilled in it
* Chamber Lid - one of the 7-1/2" by 5" by 1/4" pieces

Chamber Lid
2. Remove only the paper marked with an "X" from the Chamber Lid Front. Use a marker to place an "X" on the Plexiglas®. Now remove the paper from the other side.
3. Remove the paper from the Chamber Lid.
4. Bond the Chamber Lid Front to the Chamber Lid. The "X" on the face of the Chamber Lid Front should face outward; the "X" on the edge should be against the Chamber Lid.

Step 6a

Step 6b

Step 6c
E. Construct the Electrophoresis Chamber

1. You will need the following pieces of Plexiglas:
* Chamber Bottom - 7-1/2" by 5" by 1/4" thick
* Chamber Long Sides (2) - 7-1/2" by 2-1/2" by 1/4" thick, one of which has holes drilled in it
* Chamber Short Sides (2) - 3-7/8" by 2-1/2" by 1/4" thick

Electrophoresis Chamber
2. Remove the paper from the Chamber Bottom and lay it on a flat surface.
3. Remove only the paper marked with an "X" from the Chamber Long Side that has holes drilled in it. Use a marker to place an "X" on the Plexiglas®. Now remove the paper from the other side.
4. Remove the paper from the other pieces of Plexiglas®.
TIP: The following bonding steps require two people working together and/or the use of large rubber bands.
5. Use the Chamber Long Sides and the Chamber Short Sides to form a box on top of the Chamber Bottom; the 2-1/2" sides are perpendicular to the base. The Chamber Short Sides should be on the insides of the Chamber Long Sides. Hold the pieces in place, making sure that there are no gaps. The Chamber Long Side that has "X's" marked on it should be oriented as follows: the X on the surface should be on the outside; the X on the edge should be on the top.
TIP: Slightly inset the Chamber Short Sides from the edge of the base. This will keep the bonding agent from flowing under the Chamber Bottom and smearing it.
TIP: Use two large rubber bands to hold the sides in position while you are bonding them.
6. First bond the bottom edges of the square to the Chamber Bottom. Then turn the chamber on successive sides so that the seams you are bonding are horizontal. Remember to place bonding liquid on both the inside and outside edges of each seam.
7. Fill the chamber with water to test for leaks. Re-seal seams with the bonding agent if you find any leaks.

Step 4

Step 5
F. Place the pegs in the Electrophoresis Chamber

1. You will need the following pieces of Plexiglas®:
* Electrophoresis Chamber (from previous step)
* Gel Carrier (already constructed)
* 6 Pegs - 1/2" long pieces of 3/8" dowel or rod

Peg Placement
2. Sand the bottoms of the pegs to remove any burrs; they must be smooth to bond well.
3. Place the Gel Carrier in the center of the Electrophoresis Chamber with the Gel Carrier Sides parallel to the long sides of the Chamber.
4. Bond a peg on the bottom of the Chamber on either side of the Carrier; the pegs are centered along the two edges of the Carrier and are not tight against it. Remove the Gel Carrier from the Electrophoresis Chamber.
TIP: To bond the pegs, grasp one end with forceps/tweezers. Dip the other end into the acrylic bonding agent and then place the peg in the chamber. Remember to turn the chamber so that the surface on which you are placing the peg is horizontal.
5. Place the chamber on one short side. Bond 2 pegs on this side, approximately 3/8" up from the bottom of the chamber and 1/2" in from the sides.
6. Place the chamber on its other short side and repeat the process.

Steps 2-5

Step 4a

Step 4b

Steps 6-8

Steps 9-10

Steps 11-13

Completed box
G. Wire the Electrophoresis Chamber

1. You will need:
* 2 Insulated Banana Jacks
* 2 Solderless Banana Plugs
* 2 nuts to fit Solderless Banana Plugs
* 2 Stackable Banana Plugs
* 2 feet each of black and red Test Lead Wire
* Monel Seizing Wire or 20-gauge copper wire - 16" long piece cut in 1/2
* 2 - 1" pieces of 1/4" diameter heat shrinking tubing, one black and one red

Chamber Wiring
2. Install a Solderless Banana Plug in each of the two holes you drilled in the Electrophoresis Chamber Long Side. The Plug ends should face outward, with a nut on the inside of the chamber. Use a small adjustable wrench to help tighten the Plugs in place.
3. Place the second nut on the threaded side of the Plug but do not tighten it.
4. Use one piece of Monel or copper wire to form the electrode on the right side of the Electrophoresis Chamber. Form a small loop in one end of the wire. Place the loop between the two nuts on the Solderless Banana Plug. Tighten the nuts on the wire to form a good electrical connection. Loop the wire once around the peg closest to the Jack, then loop it around the other peg. Cut off any excess wire. Do not solder this wire into place since you will need to change it when it wears out. If you use copper wire, it will react with the electrode buffer, turning the buffer blue. Use new buffer for each gel run.
5. Repeat Step 4 on the left side of the Electrophoresis Chamber.

Chamber Wiring Banaplugs
6. Install the Banana Jacks in each of the two holes you drilled in the Electrophoresis Chamber Lid Front. Place the black Jack in the right hole and the red Jack in the left hole; the terminal ends and nuts face outward. Use a wrench to tighten the nuts.
7. Use wire strippers to strip off about 3/4" of insulation from the end of the black Test Lead Wire.
8. Thread the stripped Wire end through the hole in the metal part of the Jack and twist the stripped wire back upon itself. Make sure it feels tight.
9. Thread the piece of black heat shrinking tubing over the Test Lead Wire. Make sure to thread over the metal piece on the back of the Jack. Use an alcohol lamp or hair dryer (high heat setting) to heat the tubing to shrink it around the pieces. Do not place the tubing directly in the flame. Rotate the pieces in the heat to shrink the tubing evenly.
10. Repeat Steps 7 - 9 with the red Banana Jack, red Wire, and red heat shrinking tubing.
11. Strip about 1/2" of insulation off of the end of the black Wire (there is a Banana Jack at the other end).
12. Take a small screwdriver and unscrew the screw inside the black Stackable Banana Plug. Do not completely remove the screw. Double the stripped end of Wire on itself and thread it through the opening of the Plug. Then tighten the screw to keep the Wire in place.
13. Repeat Steps 11-12 with the red Wire and red Stackable Banana Plug.
14. Optional: Place a thin strip of black electrical tape across the bottom of the Gel Carrier under the comb. The black surface makes it easier to visualize the wells when loading the gel. Note: The black surface will make it difficult to visualize food color or dye separation in the black area; so place the electrical tape so that it does not extend past the wells toward the long end of the gel.