BME103:T130 Group 2 l2: Difference between revisions
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5. Run PCR as original<br><br> | 5. Run PCR as original<br><br> | ||
'''Benefits'''<br> | '''Benefits'''<br> | ||
With the new design the PCR machine can now run more samples at a time. Therefore, the efficiency of the system is increased. Also, there will now be | With the new design the PCR machine can now run more samples at a time. Therefore, the efficiency of the system is increased. Also, there will now be an absolute way of determining whether the door is too tight on the tubes. This allows us to be positive that the PCR machine will perform the best test on the DNA samples. | ||
<!--- From Week 4 exercise ---> | <!--- From Week 4 exercise ---> | ||
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'''Background on Disease Markers'''<br> | '''Background on Disease Markers'''<br> | ||
'''Transient Myeloproliferative Disorder of Down Syndrome''' is a combination of the diseases leukemia, down syndrome and acute myeloid. It is extremely rare and takes the life of a patient in the very early months of life. It is associated with the SNP (single nucleotide polymorphism) 121912500 on chromosome 21.<br> | '''Transient Myeloproliferative Disorder of Down Syndrome''' is a combination of the diseases leukemia, down syndrome and acute myeloid. It is extremely rare and takes the life of a patient in the very early months of life. It is associated with the SNP (single nucleotide polymorphism) 121912500 on chromosome 21.<br> | ||
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121912500<br> | http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121912500<br><br> | ||
Our PCR machine can test for multiple DNA mutations such as cancer, like in previous experiments, and now Transient Myeloproliferative Disorder of Down Syndrome.<br><br> | |||
'''Primer Design'''<br> | '''Primer Design'''<br> | ||
'''Transient Myeloproliferative Diorder of Down Syndrome:''' The forward primer of this disease is ACCGGCTG'''G'''TGGGCCCGCTG. The reverse primer that would correctly match the forward primer and not code for a diseased patient would be TGGCCGAC'''C'''ACCCGGGCGAC. The diseased allele and diseased patient will have a reverse primer TGGCCGAC'''A'''ACCCGGGCGAC. Therefore, a patient that contains the disease has an allele mutation within the pairing of G to C, it is instead G to A. This will give a positive on the PCR machine because it becomes single stranded due to the fact it cannot replicate properly. This, when we apply the SYBR green it will attach to only the single primers and the diseased patients will glow green. The replicated, normal strands, will appear clear when the SYBR green | '''Transient Myeloproliferative Diorder of Down Syndrome:''' The forward primer of this disease is ACCGGCTG'''G'''TGGGCCCGCTG. The reverse primer that would correctly match the forward primer and not code for a diseased patient would be TGGCCGAC'''C'''ACCCGGGCGAC. The diseased allele and diseased patient will have a reverse primer TGGCCGAC'''A'''ACCCGGGCGAC. Therefore, a patient that contains the disease has an allele mutation within the pairing of G to C, it is instead G to A. This will give a positive on the PCR machine because it becomes single stranded due to the fact it cannot replicate properly. This, when we apply the SYBR green to it, will attach to only the single primers and the diseased patients will glow green. The replicated, normal strands, will appear clear when the SYBR green is added because it will not be able to attach to the replicated strands. | ||
<!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. ---> | <!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. ---> |
Latest revision as of 13:46, 29 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 2 WRITE-UPThermal Cycler EngineeringOur re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.
Key Features A. Now designed to be on the side, serves as the tightening knob as in the previous design B. Glass oven-like door on the side C. Double layered to fit twice the amount of samples (32 samples) Areas marked by "*" indicate sections that will now be made from glass and therefore, transparent allowing for observation. New area for samples opens like an oven where the samples can be slid in. It will hold 32 samples instead of its original, 16. The sample trays will be placed one on top of an other when slid in onto the shelf. The glass is for seeing how tightly closed the oven lid is screwed on. Instructions
ProtocolsMaterials
Setting up the smart phone camera
Set the smart phone camera menu to the following:
1. Inactivate the flash.
DNA Measurement Protocol
Research and DevelopmentBackground on Disease Markers Primer Design
Illustration
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