BME100 f2013:W900 Group10 L4: Difference between revisions
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'''Test Run''' | '''Test Run''' | ||
On October 23, 2013, we ran the PCR machine through a test cycle. The machine ran smoothly throughout the entire process (10:06am - 11:24am) and ran very close the the rate estimated by the time to completion readout. At all points the information displayed on the PCR machine's LCD screen matched that displayed on the computer. | On October 23, 2013, we ran the PCR machine through a test cycle. The machine ran smoothly throughout the entire process (10:06am - 11:24am) and ran very close the the rate estimated by the time to completion readout. At all points the information displayed on the PCR machine's LCD screen matched that displayed on the computer. |
Revision as of 23:00, 29 October 2013
BME 100 Fall 2013 | Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help | ||||||
OUR TEAMLAB 1 WRITE-UPInitial Machine TestingThe Original Design OpenPCR is a small and relatively low cost PCR (polymerase chain reaction) machine. In the past most PCR machines were prohibitively expensive, and thus not available to most schools and enthusiasts. The designers of OpenPCR changed this by creating a very small machine containing low cost and widely available electronics (Arduinos, theremometer, LCD, ect.) and other components (wooden frame, etc.). A polymerase chain reaction, or PCR, is a chemical reaction that takes advantage of biological molecules (mostly proteins) to make billions of copies of a certain segment of a template DNA strand. A PCR reaction relies on accurately timed temperature variation to work properly. This is what a PCR machine is for. Tubes containing the PCR reactants are placed into the the heat exchange block in the PCR machine. The machine then proceeds to cycle the temperature of the PCR mixture for a user defined period of time and over a user defined temperature range. The result is massive amplification of the desired DNA segment.
When we unplugged the LCD screen (part 3) from Arduino and PCR shield (part 6), the LCD screen turned off because it was no longer receiving power or signal from the main circuit board. When we unplugged the white wire that connects the Arduino and PCR shield (part 6) to the thermometer (part 2), the machine began displaying incorrect temperature information.
On October 23, 2013, we ran the PCR machine through a test cycle. The machine ran smoothly throughout the entire process (10:06am - 11:24am) and ran very close the the rate estimated by the time to completion readout. At all points the information displayed on the PCR machine's LCD screen matched that displayed on the computer.
ProtocolsThermal Cycler Program
DNA Sample Set-up Procedure Step 1: Gather the materials necessary to conduct the lab. First extract the eight samples of the desired DNA fragments and place it into the eight different test tubes in the thermal cycler. Then gather the eight samples of 50 micro-liters of the PCR reaction mix. This mix should contain Tag DNA polymerase, MgCl2, template DNAs, Primers (forward and reverse), and dNTPs.
Research and DevelopmentPCR - The Underlying Technology In the first cycle, the temperature is raised to 95 degree Celsius which is nearly boiling point. This is when the double helix DNA separates and forms two single strands of DNA. Later on, the thermal cycler cools to about 50 degree Celsius. This causes the two single stand DNAs to join back together. However, there are a lot of primer sequences floating around due to the reaction mix. The primer sequence then grips on to the single stranded DNA and locks to it. This causes the single stranded DNA to not join with the other strand and stay separated. After that, the thermal cycler heats up to 72 degrees Celsius. This activates the tag DNA polymerase’s. Tag DNA polymerase find the end of the primer and starts to attach complimentary DNA nucleoids to both of the single stranded DNA. This is what causes the replication of DNA to take place. This marks the end of cycle two. In cycle three there are two identical DNA strands and as the cycle continues the replication continues. By the end of the cycle 30 there would be about a billion copies of DNA strand.
(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the PCR video/ tutorial might be useful. Be sure to credit the sources if you borrow images.)
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