Gel Electrophoresis and Transilluminator

User manual chapter for the Bento Lab gel electrophoresis and transilluminator module. Includes a physical specification, information on casting gels and connecting the gel box, and operation guide for the interface.

Components and Physical Layout

The gel electrophoresis and transilluminator module is on the left side of the Bento Lab system.

The gel box is made up of two parts. The base (1) is made of clear acrylic. It is used to cast gels and as a gel tank during electrophoresis. It also stores casting shutters and combs. The lid (2) is made of orange acrylic that functions as a filter for the blue light transilluminator. On the left side of the Bento Lab system (3), a red and black socket provide current for gel electrophoresis. The blue LED transilluminator (4) is located on the left side of the device.

The gel box contains several parts, including the orange lid (1) and the base (2), two dams used to create buffer zones during gel casting (3), and combs for 11 and 15 well gels (4).

Specifications

Voltage 50V – 120V
Box Dimensions91mm x 78mm
Visualisation470nm blue light and diffuser
Viewing WindowAs box dimensions
FilterAmber acrylic

User Interface

To use the Gel Electrophoresis and Transilluminator module, select it from the home screen.

At the top of the screen, the blue light transilluminator can be switched on and off. Select the light bulb button and press the orange click-dial to toggle the transilluminator on and off. 

Warning: When the transilluminator is on, do not stare directly into the blue light for prolonged periods of time.

The light intensity can also be modulated by holding the click-dial down and rotating it.

To set the voltage of a gel, first select the voltage button. Push down the orange click-wheel and keep holding it down while rotating it to change the value. Dial clockwise to increase the voltage, and counter-clockwise to decrease it. 

To start running the gel at the selected voltage, press the timer button. On the next screen, set the timer. To change the duration, push down the orange click-wheel and keep holding it down while rotating it to change the value. Dial clockwise to increase the duration, and counter-clockwise to decrease it. 

Make sure your gel is ready and connected to Bento Lab before hitting the confirm button.

If Bento Lab does not detect a current draw, or if the current draw is too high, an error message will be displayed. If no current is detected, despite the gel box being connected, this might indicate a broken platinum wire. 

When the gel is running, the remaining time is displayed on the top right position (1), and a flashing lightning bolt indicates that current is flowing (2). The clock button (3) allows for the timer to be adjusted, and the cancel button (4) can be used to turn off the power to the gel.

Casting a gel

  1. Measure out agarose. For a 1% gel, use 0.5 g with 50 mL of buffer.
  2. Mix the agarose powder with 50 mL of 0.5x TBE buffer in a microwavable flask.
  3. Once the agarose has dissolved, heat the solution in a microwave at full power for short bursts of 20-30 seconds. Swirl the solution in between bursts to mix, until the agarose is completely dissolved. Avoid overboiling the mixture, as the buffer will evaporate and you will end up with a higher concentration of agarose.
  4. Check you are working on a level surface to cast a gel with uniform thickness.
  5. Gently slide off the orange lid off the gel tank.
  6. Place the dams in the tank to cover the buffer zones around the electrodes.
  7. Select a comb and insert the comb into the holder.
  8. Once the agarose has cooled to about 55°C, it should feel hot, but not too hot to touch – add your DNA stain, and pour the melted gel into the gel tank.  
  9. Allow the gel to cool down and solidify. This takes about 30 min at room temperature, or 15 min in a cool room or a fridge.
  10. Gently remove the comb from the gel, and get ready to run the gel.

Buffers for Electrophoresis

What buffer should I use?

Bento Lab contains a mini gel electrophoresis system, therefore a higher voltage gradient than larger gel systems. Electrophoresis buffers contain ions that transmit charge to separate the DNA fragments. Higher concentration buffers transmit more charge, which is useful for large gel systems. For a mini gel system, lower concentration buffer allower better resolution of bands. For best results, we recommend running gels at 50V with 0.5x TBE.

TBE Buffer Recipe

TBE buffer is usually made as a 5X concentrated stock solution. A working solution of 0.5x TBE buffer is 45 mM Tris-borate, and 1 mM EDTA.

To prepare a 5X stock solution, add the following to 1 L of H2O:

  • 54 g of Tris base
  • 27.5 g of Boric acid
  • 20 mL of 0.5 M EDTA (pH 8)

Agarose percentage

What percentage of agarose should I use?

DNA can be resolved by size using agarose gels of various concentrations. The greater the percentage of agarose, the smaller the fragment of DNA that can be resolved. The appropriate percent agarose gel depends on the size of DNA fragment that you will be running on the gel. You will obtain good resolution of larger DNA fragments (5-7kb) with a 1% agarose gel, whereas for good resolution of small PCR products, you will need a higher percent gel.

DNA Size ResolutionPercent Agarose GelWeight Agarose
1-30 kb0.5%0.5g per 100mL
800 bp – 12 kb0.7%0.7g per 100mL
500 bp – 10 kb1.0%1g per 100mL
400 bp – 7 kb1.2%0.6g per 50mL
200 bp – 3 kb1.5%0.75g per 50mL
50 bp – 2 kb2.0%1g per 50mL

Running a gel

Bento Lab contains a mini gel electrophoresis system, therefore a higher voltage gradient than larger gel systems, as the distance used to determine voltage gradients is the distance between the electrodes, not the gel length. If the voltage is too high, you may observe band streaking. For best results, we recommend running gels at 50V with 0.5x TBE.

  1. Prepare the running buffer or use pre-prepared buffer
  2. Pour the buffer solution into the electrophoresis tank over your prepared gel until the liquid cover your gel, and the level is about 2-3 mm above your gel.
  3. Carefully load a molecular weight ladder into the first lane of the gel.
  4. Load your samples into the remaining wells of the gel.
  5. Gently slid the orange lid onto the gel tank until it clicks shut.
  6. Set the voltage to the desired electrophoresis voltage for your protocol. To make changes to the voltage, select the voltage value button. Push down the orange click-wheel and hold down whilst rotating to change the value. Dial clockwise to increase the voltage, and counter-clockwise to decrease. Release the orange click-wheel once you have reached the desired voltage.
  7. Set the desired time by selecting the time value, pushing down and rotating the orange click-wheel.  
  8. Confirm your settings by clicking on the tick on the right, and set the gel to run.
  9. Run the gel until the dye line has travelled down about 75% the length of the gel. A typical run time with Bento Lab is about 30-45 minutes, depending on the gel concentration and voltage.
  10. Wait until the run has finished, or cancel the run. Disconnect the electrodes from the power source, and then carefully remove the gel from the gel box.
  11. Place your gel on the transilluminator, and select the transilluminator button to turn the blue light on to visualise your bands.