Blue Light DNA Transilluminator

Gel electrophoresis arises as an efficient method for comparing various macromolecules such as DNA and RNA based on their size and charge properties. The molecules under analysis are pipetted within a gel made of agarose. The gel is then placed between two electrodes having opposite charges and submerged within an electrolyte buffer solution. An electric field is consequently created once voltage is applied to the electrodes. As a result, the negatively charged molecules gravitate towards the positively charged anode by the action of the electric field. The difference in size becomes apparent as smaller molecules will travel through the gel matrix faster than larger molecules. Further details about the protocols can be found elsewhere. ***

Once the action of the electric field has separated the molecules, a DNA transilluminator is used to observe the location of each molecule within the gel matrix. In detail, the addition of a staining dye within the gel allows the molecules to be fluorescently excited by light having wavelengths within the UV or blue region of the electromagnetic spectrum. Various staining dyes exist with different excitable wavelengths *. A transilluminator is therefore critical for reaching meaningful conclusions from the gel-electrophoresis procedure. However, as demonstrated below, such devices tend to be highly expensive.

Commercially available transilluminators:

• Thermofisher Scientific --> Price: 2200$
• VWR International --> Price: 742$
• Analytik Jena --> Price: 2337$

Students or small laboratories with limited financial support for scientific investigations are often forced to search for alternative methods for analyzing their gels. The present project demonstrates the design and assembly of a DNA transilluminator system using easily accessible components at a respectable cost. The project can be tackled by young students aiming at gaining practical skills in building laboratory equipment or experienced scientists searching for a rapid and cost-efficient method for analyzing gels. The complexity of the project is kept at a minimum. Further modifications can be undertaken to improve the performance of the device. No professional experience in electronics design or software programming is needed.

The project is divided as follow:

1. Designing and 3D printing the required plastic parts.

2. Assembling the mechanical components.

3. Assembling the electronics components as well as programming the microcontroller.

4. Testing the device and proposing potential improvement.

1. Designing and 3D printing the required plastic parts:

The design procedures have been separated into three sections:

• Cover (Screen_Perimeters.stl + cover.stl)
• LED Box (Illuminator_Box.stl + Transparent_Glass.stl)
• Electronic Box (Electronics_Box.stl + Box_Cover.stl)

The design of each component was created within Fusion 360. The STL files and the Fusion 360 model can be downloaded from the appropriate section below.

2. Assembling the mechanical components:

1.1 --> A small amount of Krazy Glue is deposited onto the black perimeter surface (Labelled as #1).

1.2 --> The orange UV shield (Labelled as #2) is gently deposited onto the black perimeter component having a small amount of glue onto the surface. Wait 5 minutes before proceeding to the next step for the glue to solidify.

1.3 --> Apply a small amount of Krazy Glue onto the interior perimeter of the black upper cover (Labelled as #3). Gently align the upper cover onto the orange UV shield. Wait 5 minutes for the glue to fully solidify.

1.4 --> Briefly measure two equally distanced positions on the exterior of the LED box for gluing two cover hinges. The measurement is only for aesthetic purposes and does not necessarily affect the performance of the unit. Next, apply a small amount of Krazy Glue onto the two selected areas and gently depose one side of the door hinge. Be careful not to apply any glue onto the rotating area. Wait 5 minutes for the glue to be fully solidified.

To maximize the reflection of light from the LED towards the UV orange shield, a total of 5 mirror metallic pieces are cut and glued at the bottom of the LED box.

2.1 --> Carefully measure and mark the dimension of the bottom surface of the box onto the mirror surface of the sheet. Then, gently cut with scissors the desired area of interest.

2.2 --> Proceed similarly by measuring each side of the LED box and marking the measurement onto the mirror glassy sheet. Next, cut with scissors a total of 4 pieces that will cover each inner side of the box.

2.3 --> By applying Krazy glue onto each inner side of the box, gently glue each metallic component.

2.3 --> To allow the wires from the LED to connect to the electronic circuit located within the electronic box, a small hole having a diameter of 0.3'' is created using a tool of preference. A conventional drill has been used for the purpose.

2.4 --> To diffuse the light emitted by the series of LEDs, the plastic PLA sheet previously printed is deposited on the upper surface of the box. Different thicknesses could be tested to optimize the diffusion of light throughout the PLA plastic sheet.

3.1 --> Drill a hole on the right side of the electronic box to allow the insertion of the power jack. Ensure to select the hole diameter following the size of the power jack.

3.2 --> Apply a small amount of Krazy glue onto the back perimeter of the box. Gently align the box onto the LED box. Wait 5 min for the glue to solidify. Do not glue the cover onto the electronic box as the circuit components will have to be soldered and inserted.

3. Assembling the electronics components as well as programming the microcontroller:

• Solder the Arduino Nano onto the PCB board.
• Utilizing a black jumper wire, connect the ground pin of the power jack to the ground pin of the switch.
• Utilizing a red jumper wire, connect the power pin of the jack to the middle power pin of the switch. This will allow the LED indicator of the switch to be lit up once power is turned ON.
• Solder the green data line from the LED strip to digital PIN6 of the Arduino board.
• Solder the white data line from the LED strip to the GND PIN of the Arduino board.
• Solder the RED power line from the LED strip to the remaining power PIN of the switch.
• Solder an additional jumper wire from the power PIN of the switch to the VIN PIN of the Arduino board. This will allow the input voltage from the jack to power the Arduino.

- Arduino Programming

Library Required: Adafruit NeoPixel

Software from the Adafruit NeoPixel library: strandtest

If not already downloaded, the Adafruit NeoPixel library can be download by following:

• Tools
• Manage Libraries
• Searching with keyword --> NEO
• Click install on--> Adafruit NeoPixel

As demonstrated in the image provided, the colour dynamics of the LED strip can be adjusted by adding "//" to the lines of code associated with the undesired colour. Since only blue is desired for the application, all other lines are commented by adding --> "//."

void loop() {
  // Fill along the length of the strip in various colors...
  //colorWipe(strip.Color(255,   0,   0), 50); // Red
  //colorWipe(strip.Color(  0, 255,   0), 50); // Green
  colorWipe(strip.Color(  0,   0, 255), 50); // Blue

  // Do a theater marquee effect in various colors...
  //theaterChase(strip.Color(127, 127, 127), 50); // White, half brightness
  //theaterChase(strip.Color(127,   0,   0), 50); // Red, half brightness
  //theaterChase(strip.Color(  0,   0, 127), 50); // Blue, half brightness

  //rainbow(10);             // Flowing rainbow cycle along the whole strip
  //theaterChaseRainbow(50); // Rainbow-enhanced theaterChase variant
}

4. Testing the device and proposing potential improvement:

• The thickness of the transparent PLA plastic sheet can be adjusted to provide optimal light diffusion.
• Additional LED strips could be added to increase the light intensity.
• Selecting LED strips with the ability to emit within the UV range of the electromagnetic spectrum would allow greater flexibility during the selection of staining dye.