BME100 f2013:W1200 Group13 L4
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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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LAB 1 WRITE-UP
Initial Machine Testing
The picture above shows what the OpenPCR machine looks like while running and connected to the computer. The machine case is made of wood panels which contains the actual hardware of the device. The smaller box located on the top is the lid of the OpenPCR machine. This contains a 16-tube PCR block which is where the test vials are placed in order to complete the test run. The top part of the lid has a heat plate that heats the vials and also seals the experiment. Inside of the main body of the OpenPCR machine there is a heatsink, processor, led screen, and copper wire connections. The processor has a circuit board that recieves the data from and computes the calculations. The heatsink dispersses the heat and the fan attached cools down the device in order to avoid overheating. The led screen displays the data specifically the numbers of tests run and temperature. The machine also has an USB port and power connection in order to power the device and connect it to the computer in order to run the tests.
Experimenting With the Connections
When we unplugged the LED screen (part 3) from the circuit board(part 6), the machine didn't display anything on the screen because this connection is what allows the power to connect to the led screen. When we unplugged the white wire that connects (part 6) to (part 2), the machine lost the ability to record data and to sense the heat change in the machine.
Our OpenPCR machine passed the testing that we conducted in class. We began the testing at 12:50 pm, and at 1:40pm the machine had run 19 out of 35 tests. When we concluded the experiment the temperature according to the screen on the device was 95 degrees Celsius, and had an ETA of 48. The test ran very smoothly for the first time use and we didn't encounter problems with the machine not working properly. The device was plugged into the computer and then we opened the program in order to start the tests. Then after entering in the information given we began running the test. There were no issues with the program or the machine. )
Thermal Cycler Program
DNA Sample Set-up
DNA Sample Set-up Procedure
The PCR reaction , 50uL each. the mix contains Taq DNA polymerase, MGCl2, and dNTP's.
DNA/ primer mix
Each mix contains a differant template DNA all tubes have the same forward primer and reverse primer.
Research and Development
PCR - The Underlying Technology
At the beginning of the thermal cycling, the samples are heated for 3 minutes at a temperature of 95 degree Celsius, and the heat makes the double-helix unwind and separate into two single stranded DNA molecules. Afterwards, the temperature is brought down to 57 degrees Celsius, the temperature change makes the primer attach to the target sequence. Once again, the temperature is brought up, this time to 72 degrees Celsius, this activated the TAQ polymerase and attaches to the primer that is attached to the single DNA strand and adds complimentary nucleotides to the strand until it detaches. When adding complimentary base pairs, the adenine (A) bonds to thymine (T) and the cytosine (C) bonds to guanine (G). Now, we have a copy of the specific sample we wanted, in this case the cancer mutations. Doing this helps because the resulting product is almost entirely made up of the cancer mutation with very few impurities, and scientists can work and figure out what is wrong with that piece of DNA and try to solve the problem.