BME100 s2017:Group7 W8AM L4: Difference between revisions
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'''Background: About the Disease SNP''' | '''Background: About the Disease SNP''' | ||
<!-- INSTRUCTIONS: This content is from PCR Lab B. Write a summary, at least five sentences long, about the disease SNP in your own words. -- | <!-- INSTRUCTIONS: This content is from PCR Lab B. Write a summary, at least five sentences long, about the disease SNP in your own words. --><br> | ||
A single nucleotide polymorphism (SNP) is a DNA sequence variation in one base pair which does not normally occur in other members of the same species. The specific SNP of interest for this laboratory has a reference code rs121908757, and specifically points to a SNP where an adenine nucleotide, in most of the species, becomes a cytosine nucleotide. This small and seemingly minute change in the genome pathogenic and affects the homo sapiens species by greatly increasing the chance of developing the disease cystic fibrosis. This genetic order most commonly causes damage to the lungs and also the digestive system. This SNP occurs on chromosome seven, results in approximately 70% of cystic fibrosis cases. | A single nucleotide polymorphism (SNP) is a DNA sequence variation in one base pair which does not normally occur in other members of the same species. The specific SNP of interest for this laboratory has a reference code rs121908757, and specifically points to a SNP where an adenine nucleotide, in most of the species, becomes a cytosine nucleotide. This small and seemingly minute change in the genome pathogenic and affects the homo sapiens species by greatly increasing the chance of developing the disease cystic fibrosis. This genetic order most commonly causes damage to the lungs and also the digestive system. This SNP occurs on chromosome seven, results in approximately 70% of cystic fibrosis cases. | ||
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'''Primer Design and Testing''' | '''Primer Design and Testing''' | ||
<!-- INSTRUCTIONS: Write a short summary of the results of your primer test. Underneath your summary, include a screen capture of the results web page. You may crop the image so that it only includes the relevant information. --> | <!-- INSTRUCTIONS: Write a short summary of the results of your primer test. Underneath your summary, include a screen capture of the results web page. You may crop the image so that it only includes the relevant information. --> | ||
[[Image:ResultsLab4.png|center|700px|Primer and Design Testing Toolbar Results]]<br> | |||
<center>Primer and Design Testing Toolbar Results</center><br><br> | |||
Primer design consists of being able to find the forward primer and the reverse primer reading them from 5’ to 3’. The non disease forward primer is 19 base pairs in front of where the error in the code is for cystic fibrosis and that one base pair making it 20 total base pairs for the forward primer. The non disease reverse primer starts exactly 200 base pairs in front of the base pair mutation point for cystic fibrosis. Of course this base pair is not mutated in the non disease primers but it is used as a reference point. After adding 200 to the numerical position of the SNP the reverse primer can then be found. In our case the forward primer ends at position 117587799 and the reverse primer ends at 117587999. At that final position we can read from 5’ to 3’, 20 base pairs and obtain the non disease reverse primer. When these primers were plugged into the the genome site, it was successful and these primers were found to be on chromosome 7, and 220 base pairs long. When the disease mutation was used, changing the CGT to AGT, the primers were not found probably because this is a mutation and it is not expected to be on a healthy human genome. <br> | |||
Latest revision as of 22:30, 21 March 2017
BME 100 Spring 2017 | 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 4 WRITE-UPProtocolMaterials
The first step in the DNA sample setup is to take the extracted DNA and put a sample of it into the PCR tube. After this is complete, a sample of Primer 1 will then be taken from its capsule and put into the PCR tube along with the DNA sample. Now, Primer 2 will be added to the PCR tube which will eventually attach into the second site. Next, an excess amount of nucleotides will be added to the PCR tube in order to continue building DNA strands. The final component that will be added is the DNA Polymerase, an enzyme that will build back the strands of DNA using the surrounding nucleotides. Finally, the PCR tube will be placed into a DNA Thermal Cycler, which is a machine able to control the temperature of the PCR environment and dictate key changes in the reaction.
1) Set the DNA Thermal Cycler to 100°C
4) The sample is then kept at 72°C for 2 minutes
Research and DevelopmentPCR - The Underlying Technology Component Functions Thermal Cycling Process DNA nucleotides Base Pairing Occurrence
SNP Information & Primer DesignBackground: About the Disease SNP
Primer design consists of being able to find the forward primer and the reverse primer reading them from 5’ to 3’. The non disease forward primer is 19 base pairs in front of where the error in the code is for cystic fibrosis and that one base pair making it 20 total base pairs for the forward primer. The non disease reverse primer starts exactly 200 base pairs in front of the base pair mutation point for cystic fibrosis. Of course this base pair is not mutated in the non disease primers but it is used as a reference point. After adding 200 to the numerical position of the SNP the reverse primer can then be found. In our case the forward primer ends at position 117587799 and the reverse primer ends at 117587999. At that final position we can read from 5’ to 3’, 20 base pairs and obtain the non disease reverse primer. When these primers were plugged into the the genome site, it was successful and these primers were found to be on chromosome 7, and 220 base pairs long. When the disease mutation was used, changing the CGT to AGT, the primers were not found probably because this is a mutation and it is not expected to be on a healthy human genome.
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