Introduction: Standing Gel Electrophoresis Chamber

Picture of Standing Gel Electrophoresis Chamber

We want to make a electrophoresis chamber with the following features:

1. Use blue light instead of UV to trigger the fluorescence of the dye.

2. Stands on the bench with adjustable angle so it is easy to view.

3. Magnetic hinge that won't break.

4. There is no fog on the observation window.

5. Power consumption is low.

6. It is cheap.

All the design files as well as the Bill of Material is attached.

We hope our work can inspire more interesting machines using magnets.

Acknowledgement to:

David Ma, Clark Zhang (Authors, University of Maryland)

Zheng Zhou (George Mason University)

Dr. Sarah Bergbreiter (University of Maryland)

Dr. Yuntao Wu (George Mason University)

Step 1: List of Parts

Picture of List of Parts

1. Front panel:

This is a transparent plastic panel glued to the main chamber body. It has a horizontal groove on the upper part to place the electrode wire for the reaction. The front surface of the panel is covered with filter material to block the blue light from the light source while letting the green fluorescent light from samples pass through.

2. Gel cassette:

This is a commercial pre-cast gel cassette.

3. Chamber frame:

LED shooting from behind

The LED panel is placed in the rear part of the frame, separated from the front chamber for electrical isolation and waterproof. Heat dissipation is also another concern for this design approach since when voltage is applied to the electrodes, the buffer solution are slowly heating up which could affect negatively on the experiment results. Shielding from the LED panel block heat radiation to penetrate through to the front chamber.

Placing the LEDs on the side of the front viewing chamber as a conventional approach would require complicated waterproof and power supply module which far superseded the advantage.

The deflector along with filter and shielding material are also integrated into the rear chamber as explained in the later section.

Configuration of electrodes

The voltage applied to the electrodes for electrophoresis experiment are typically at 90 V, 150 mA. Since they are immersed into the buffer solution, good insulation must be provided by the back panel, which is located in the middle of the chamber frame, separating front and rear chamber. The position of the electrodes are critical to electrophoresis experiment since only a vertically symmetric electric field can drive the molecules in a straight line, yielding measurable results. Otherwise the molecules might follow a skewed path in the gel thus render the results invalid. For our design we placed the cathode at the top and anode at the bottom since DNA molecules are negatively charged. Both electrodes are made of platinum of equal length, soldered with a copper wire covered with insulation, which is then soldered onto the banana connector on the back of the case.

4. Back panel of the chamber, holding the deflector and the circuit board.

5. Cap

6. Deflector

7. LED panel

8. LED back panel

9. Support frame

10. Leg

11. Feet

Step 2: Fabrication of the Deflector

Picture of Fabrication of the Deflector

Deflector: This is a piece of transparent material with patterns on both

sides in order to deflect the light from LED to cover the entire area at uniform luminosity without losing too much power. A blue filter film is attached to the chamber side of the deflector to block undesired light in the spectrum which does not trigger the fluorescence. A heat shield layer is applied between the deflector ring layer and the filter to block heat radiation passing through.

The LED side of the deflector has a dent for each LED to diffuse the normal incident light into a more dispersed light cone. The chamber side of the deflector has concentric grooves for each LED light cone to further disperse the light in order to shine the sample area uniformly.

We use 1/8" cast acrylic to make the deflector, using a 50W CO2 laser cutter.

The settings are as follows:

Ring side: 30%power; 100% speed; 1000 PPI; 0.2" z-axis

Dent side: 100%power; 10% speed; 1000 PPI; 1.2" z-axis

Step 3: Fabrication of Magnetic Hinge

Picture of Fabrication of Magnetic Hinge

We proudly introduce the magnetic hinge we developed for this project, for it is both well functional and entertaining.

We laser cut 1/4" cast acrylic sheet and glue neodymium magnet into it. Make sure the orientation of the magnets are towards the same direction.

This hinge structure can be used on other applications that don't have a concern with the magnets.

You can press the hinge and let it jump!

Step 4: Choice of Filter & Dye

Picture of Choice of Filter & Dye

The dye we use is Sybr, and here is the link.

https://www.thermofisher.com/us/en/home/life-scien...

The filter has two parts, the background filter and the front panel filter. The background filter is between the LED panel and the main chamber, and it only allows the wavelength that triggers the fluorescence to pass. The front panel filter is on the top of the observation window, and it blocks the blue light from the LEDs, letting the fluorescence pass.

Background filter: 2 layers of Lee 716 blue film filter

Front panel filter: 2 layers of Lee 767 yellow/amber film filter.

Step 5: Fabrication of the Chamber

The chamber is 3D printed.

See the stl file attached

Step 6: Circuitry

Step 7: All Design Files

Comments

DanYHKim (author)2017-09-27

I have found that graphite pencil 'leads' can be used as electrophoresis electrodes. There are leads, sometimes called 'engineering leads', used in mechanical drafting pencils. Here's the description of one from Amazon:

Staedtler Mars Carbon Lead, 12 x 2mm, HB (200-HB)

Depending on the hardness of the lead, the rod will contain more or less graphite, which affects conductivity. The standard number 2 lead worked well for me.

DanYHKim (author)2017-09-27

Oh, it is also possible to make a simple 120 V power supply by running AC power through a circuit with a bridge rectifier in it. The rectifier blocks the reverse current of AC, resulting in a 120 V pulsed power supply. Be very careful constructing such things, because if you don't do it with care, you might just kill yourself. But with the help of an experienced electronics guy, power supplies can be made very cheaply.

DanYHKim (author)2017-09-27

I once made a Western blotter using graphite motor brushes as the electrodes. Usually, we see these items in very small sizes, but some motors are huge, and so very large plates of graphite can be obtained from some parts suppliers. It worked quite well.

DIY Hacks and How Tos (author)2017-09-24

Awesome! I love DIY science.

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