BME103:W930 Group4 l2

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Name: Christian Vargas
Name: Jake Krammer
Research and Development
Name: Jan Simper
Research and Development
Name: Renaad Mohammed
Name: Lauren Allison
Open PCR Machine Engineer(s)
Name: Justus Vangor
Open PCR Machine Engineer(s)


Thermal Cycler Engineering

Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.

System Design

PCR with Drawers.PNG

Key Features


The new casing will become larger to implement a set of two drawers in the front. They will be placed near the top of the case and in the middle of the front panel. These will hold the additional sample plates being added to the design, providing for higher testing numbers and easier separation of sample groups.

Heat Sinks/Fans/Mounting Plates:

The new design will have two of heaters attached to two fans, one corresponding to each drawer of sample plates and placed beneath them, just as they were placed beneath the original heat lid. Adding additional heating and cooling elements will allow the machine to adjust the temperature of more samples, more quickly. Similarly, another mounting plate will be added to correct for the increase in sample plate size. The new, larger mounting plate will accommodate all the additional PCR blocks.

PCR Blocks/Square Aluminum Adapter Plates/Thermal Pads:

As the main component of the new design, sample plates have been added. Within the framework of each drawer, and placed atop the mounting plate which has been adjusted for size, four square aluminum adapter plates will be laid down. On top of them, four ceramic peltier heaters, followed by four PCR blocks (each of which contains 16 wells). All these elements will be lined with thermal padding. This expands the sample number from 16 to 128 spread across two drawers, while still maintaining accuracy in temperature fluctuation between sample sets.


Once the new sample plates have been placed within the mounting plate, along with all the thermal padding and heating elements, additional insulation will need to be added. Around the perimeter of the four consecutive plates, white insulation strips will be placed just as before around the single plate to ensure that the temperature of the samples is not lost through the PCR block.


All instructions from the original PCR design will be followed with these new-design exceptions:

The Core:

Find these parts-

  • Heat Sinks (2) and Fans (2)
  • Small screws (16)
  • Metal Arms (4 left, 4 right)

1) The 8 heat sink arms have plastic clips. These clips need to be removed. 2) Find your pliers and break off 4 of the black plastic tabs. Avoid bending the metal arm. 3) Remove the stickers on top of the heat sinks that read "Please peel off label". 4) Use 4 aluminum screw to mount the arms onto the heat sinks. Make sure all the arms angle down. 5) Repeat for the remaining arms.



PCR Protocol

DNA Measurement Protocol

Research and Development

Background on Disease Markers

Our group decided to look at two different diseases, metabolic syndrome and cardiovascular disease. Metabolic syndrome is a name for a group of risk factors that occur together and increase the risk for coronary artery disease, stroke, and type 2 diabetes. Cardiovascular disease refers to any disease that affects the cardiovascular system, principally cardiac disease, vascular diseases of the brain and kidney, and peripheral arterial disease. The associated mutation for metabolic syndrome was rs1800206, and for cardiovascular disease it was rs1801253.

Primer Design

Forward Primer:

Reverse Primer: 5'TCACAAGTGCC3'