Transilluminator for DNA Gel Electrophoresis

How do you visualize DNA that you have separated by gel electrophoresis? Typically, the DNA is run in the presence of a fluorescent DNA stain that will light up when illuminated with a uv or blue light.

For the simple gel electrophoresis unit I had made before, I needed a transilluminator that could be placed on the gel box so that I could see the DNA. The approach I used was to illuminate from the top rather than the bottom so that most of the blue light would not enter the camera only the fluorescent light from the dye bound to DNA would. The final transilluminator is shown with an image of a 100 bp size standard run on a 1% agarose gel in Tris Acetate buffer. The lowest band is 100 bp long, the 2nd band above that is 200 bp long and so on.

The video shows the transilluminator in operation and summarizes the construction of the unit.

The plan for the transilluminator is shown in the second image. An amber filter would block the blue light from the LEDs but would let the orange or green fluorescence light from the DNA-dye complex through.

Construction of the transilluminator was divided into three parts.

1. The box to hold the illuminating LEDs

2. LED holder to hold the LEDs and shine the light in the right direction

3. Power supply to feed the LEDs

Step 1: Making the Transilluminator Box

The box was a simple rectangle made out of unidentified plastic bought from the Tap Plastics surplus bin in Mountain View, CA. I checked the heat tolerance of this plastic by placing a piece inside a cup and microwaving it. The plastic did not soften. I had also bought samples of transparent acrylics that were pre-cut at 4 inches square. This determined the dimensions of my viewing window. The four top surfaces of the box were cut on my bandsaw, edges were flattened with sandpaper and the pieces glued together as shown. For fusing the plastics together, the Goof-off cleaner worked very well. Re-enforcing bars were glued to the bottom to strengthen the top of the box and also support the viewing window. Two sides were then cut and glued to the top panel. A hole was cut into the side of the box for the female cable socket to feed power to the LEDs. The blue panel in the images was used to make sure the sizes and assembly was correct. I cut and glued the remaining pieces to make the box. The overall top dimensions are not square with one set of sides being smaller than the other so that it would fit on my DIY gel box.

Step 2: Making the LED Holder and Wiring the LEDs

I had rescued 15 high power blue LEDs from a blue LED light. These LEDs were rated at 700 mA so quite powerful. I had also rescued an LED driver board that could feed three sets of 5 high power LEDs. I decided to have two sets of LEDs shining downwards on the gel so glued 8 LED's onto a piece of L-shaped aluminum strip that I had anodized. Seven LEDs were then glued to another L-shaped strip. Did not have heat conductive epoxy so used a very thin layer of construction adhesive. The strip would act as a reflector as well a heat-sink for the LEDs.

The LEDs were wired as shown in the diagram. LEDs were daisy chained in sets of 5 LEDs per chain with the positive tab for one LED being directly soldered to the negative tab of the next LED. A total of 3 chains were prepared to be compatible with the driver board. Had to work really carefully due to the closeness of the LEDs but managed to get the wires connected. The aluminum strip was glued onto plastic wedges that held the L-strips at an angle. The remaining two sides were now glued in.
The three sets of ground wires from the LED chains were brought together and soldered onto a brown wire which was led to a small toggle switch for power, that is, the power switch was placed on the ground connection. The three positive wires were bundled behind the aluminum L-strip and passed through a hole for the multipin connector. Two pins were connected to one LED chain positive wire so a total of 6 pins were used for the three LED chains. The negative (ground) wire from the power switch was connected to the metal cylinder tab and to the central pins.

The bottom plastic strips were finally glued into place. The unfinished box with the LEDs, switch and the multipin socket is shown in the last image.

Step 3: Making the Transilluminator Power Supply

Already had two main components for the power supply. An LED driver board that would provide a constant current to the three sets of five LEDs. And an 18V 1.5A power supply that would provide power to the LED driver board. Both these boards would just about fit into a small project enclosure. So cut the required holes into the enclosure: for the IEC socket, for a toggle switch for power and for the LED supply cable. The Live lead from the AC IEC socket was wired to the power switch and the other terminal of the power switch was soldered to the board. Neutral was directly soldered to the board. Earth was not used. Connections were checked with an ohmmeter to make sure that there were no shorts. The output of the PSU was checked to be at 18V. The + 18V and 0V sensed outputs were then soldered to the LED driver board power inputs (showed covered with white heat shrink tubing). An ethernet cable was used as the power cable for the LEDs. A pair of wires from the 8 wires in a shielded ethernet cable was connected to each of the three LED outputs. The shield and the remaining two ethernet wires were connected to the 0V. The other end of the ethernet cable was terminated into a multipin male socket connected with two pins assigned for each LED string plus the 0V. The multipin socket was assembled, sealed with black hot glue and covered with a cable strain relief. Checked the work with an ohmmeter throughout this process to keep check of wires, shorts and open connections. The cable was then plugged into the transilluminator board - worked!

Step 4: Using the Transilluminator

The transilluminator is placed on an agarose gel that has been electrophoresced or on top of the DIY electrophoresis tank and the blue light turned on to see the fluorescence.

An image of a gel with 100 bp size standards is shown in the last image. The gel was placed on a dark surface and the transilluminator placed on that, turned on and an image was taken with a cell phone camera in a room with subdued lighting.