BME103:T930 Group 4: Difference between revisions
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'''Specific Cancer Marker Detection - The Underlying Technology'''<br> | '''Specific Cancer Marker Detection - The Underlying Technology'''<br> | ||
When replicating DNA, one must make sure the primer is specific to a certain gene. In this case, we studied the change in a base sequence located on Chromosome 22. The location of the sequence change, known as rs17879961, was at 542 | When replicating DNA, one must make sure the primer is specific to a certain gene called checkpoint kinase 2. In this case, we studied the change in a base sequence located on Chromosome 22, which would result in the potential development of cancer. The location of the sequence change, known as rs17879961, was at 542, and again at 671. This alteration changes the codon ATT to ACT (thymine to cytosine), changing the coded protein from isoleucine to threonine.<br> | ||
Only certain people will test positively for this test. This is because during the Polymerase Chain Reaction (PCR) detection, the primer will only recognize a certain sequence. So with the change from ATT to ACT, the primer will seek to recognize the said cancer-associated sequence. In this case, the sequence it must recognize is 3' ACATACG</b>T</i>C</i>A<b/>CATTCTCAAA 5'. The bold portion represents the changed protein codon, while the italicized letter represent the missense mutation, or change of a single nucleotide. So, if a patient has cancer, they will have this sequence described, and therefore, the PCR reaction will take place because the complement primer will bind to the site and replicate the DNA. However, if the patient does not have cancer, they will not have this changed base, nor the sequence for the primer to bind to. Therefore, no replication will occur. | |||
(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 OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.) | (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 OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.) |
Revision as of 18:23, 12 November 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
OUR TEAMLAB 1 WRITE-UPInitial Machine TestingThe Original Design
When we unplugged PCB Board of LCD from PCB of open PCR Circuit Board, the LCD display would turn off. When we unplugged the white wire that connects PCB of open PCR Cicuit Board to the temperature sensor wire, the temperature reading of the machine dropped drastically.
10/25/12 Testing the Open PCR for the first time was more complicated than we expected. Our Open PCR had technical difficulties that hindered its performance. Our samples took over 2 hours to cycle completely compared to other Open PCRs which took about 1 1/2 hours. In the end, the machine performed its task successfully. The software interface of the Open PCR was easy to understand and use. The LCD screen display also made it easy to monitor the progress of the test.
ProtocolsPolymerase Chain Reaction Polymerase Chain Reaction (PCR) is a process used to amplify DNA by making millions of copies of a particular sequence.
The PCR master mix is GoTaq® Colorless Master Mix, a premixed ready-to-use solution containing bacterially derived Taq DNA polymerase, dNTPs, MgCl2 and reaction buffers at optimal concentrations for efficient amplification of DNA templates by PCR.
Eight samples were ran. The first sample was a positive control for the gene being replicated. There were three samples from patient number 87998, a 48 year old female patient. There was also a negative control for the gene being replicated. There were three samples from patient number 21822, a 45 year old male patient. Flourimeter Protocol In order to prep for our measurements we took the following steps:
Research and DevelopmentSpecific Cancer Marker Detection - The Underlying Technology When replicating DNA, one must make sure the primer is specific to a certain gene called checkpoint kinase 2. In this case, we studied the change in a base sequence located on Chromosome 22, which would result in the potential development of cancer. The location of the sequence change, known as rs17879961, was at 542, and again at 671. This alteration changes the codon ATT to ACT (thymine to cytosine), changing the coded protein from isoleucine to threonine. (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 OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)
Results
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