BME103 s2013:T900 Group1: Difference between revisions
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==Protocols== | ==Protocols== | ||
PCR, or Polymerase Chain Reaction, is a method of amplifying a particular segment of DNA by way of selective replication. If the sequence of the target DNA segment is known, primers can be created from the complimentary base pairs at each end of the target segment. A forward as well as a reverse primer is required so that each double strand of DNA results in two double strands of DNA at the end of each cycle (as Taq DNA Polymerase only works in one direction, it needs a primer at the beginning of both strands in order to copy both). To complete PCR, a DNA sample (containing the target DNA segment) must be mixed with the primers (both forward and reverse as discussed above), Taq DNA Polymerase, dNTP's (free base pairs to be used as the building blocks in the new DNA put together by the polymerase), and MgCl<sub>2</sub> (a required substrate for the polymerase to use the dNTP's).<br> | |||
This solution is then subject to multiple cycles of varying temperatures. The temperature at each stage is chosen to optimize the desired activity of the various ingredients. First, the solution is heated to 95°C for 3 minutes to denature the double stranded DNA into two single strands. This makes the nucleotides available to attaching to the primers (which are much more abundant in the solution than the initial strands of DNA) when the solution is cooled to 57°C. After 30 seconds, the solution is brought up to 72°C, the temperature at which the activity of Taq DNA polymerase is optimal. This temperature is held for 30 seconds while Taq DNA polymerase attaches to the primers and replicates the DNA. This single cycle results in twice as many strands of double-stranded DNA as was put in. The cycle is repeated 35 times with each temperature being held for 30 seconds each. When sufficient copies of the DNA segment have been made, the temperature is decreased to 4°C to stop the reaction. <br> | |||
A step-by-step break down of the procedure follows.<br><br> | |||
'''Thermal Cycler Program'''<br><br> | '''Thermal Cycler Program'''<br><br> | ||
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# 72°C: ''DNA polymerase activates and replicates target segment of DNA.''<br> | # 72°C: ''DNA polymerase activates and replicates target segment of DNA.''<br> | ||
'''Stage 3'''<br> | '''Stage 3'''<br> | ||
Final Hold 4°C for 3 minutes: ''PCR reaction is stopped''<br><br> | Final Hold 4°C for 3 minutes: ''PCR reaction is stopped.''<br><br> | ||
'''DNA Sample Set-up'''<br> | '''DNA Sample Set-up'''<br> | ||
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'''DNA Sample Set-up Procedure''' | '''DNA Sample Set-up Procedure''' | ||
# 8 reaction tubes were provided to us, each containing 50μL of PCR reaction mix | |||
# All reaction tubes were labeled according to the table above in order to avoid swapped results | # All reaction tubes were labeled according to the table above in order to avoid swapped results | ||
# 50μL of each DNA sample was added to the correspondingly labeled reaction tube using a new pipette tip for each transfer | # 50μL of each DNA sample was added to the correspondingly labeled reaction tube (using a new pipette tip for each transfer in order to avoid cross-contamination between samples) | ||
# The reaction tubes were placed into the | # The reaction tubes were placed into the thermocycler | ||
# The thermocycler program detailed above was run so that PCR would occur in each reaction tube | |||
'''PCR Reaction Mix'''<br> | |||
50μL of each of the following:<br> | |||
* Taq DNA polymerase | |||
* MgCl<sub>2</sub> | |||
* dNTP's | |||
* forward primer | |||
* reverse primer | |||
'''DNA/Primer Mix'''<br> | |||
50μL of each of the following:<br> | |||
* Extracted sample of a particular patient's DNA | |||
* forward primer | |||
* reverse primer | |||
<br><br> | <br><br> |
Revision as of 13:44, 22 March 2013
BME 103 Spring 2013 | 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 (part 3) from (part 6), the machine ... (did what? fill in your answer) When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer)
(Write the date you first tested Open PCR and your experience(s) with the machine)
ProtocolsPCR, or Polymerase Chain Reaction, is a method of amplifying a particular segment of DNA by way of selective replication. If the sequence of the target DNA segment is known, primers can be created from the complimentary base pairs at each end of the target segment. A forward as well as a reverse primer is required so that each double strand of DNA results in two double strands of DNA at the end of each cycle (as Taq DNA Polymerase only works in one direction, it needs a primer at the beginning of both strands in order to copy both). To complete PCR, a DNA sample (containing the target DNA segment) must be mixed with the primers (both forward and reverse as discussed above), Taq DNA Polymerase, dNTP's (free base pairs to be used as the building blocks in the new DNA put together by the polymerase), and MgCl2 (a required substrate for the polymerase to use the dNTP's). Stage 1
Stage 3 DNA Sample Set-up
DNA Sample Set-up Procedure
PCR Reaction Mix
DNA/Primer Mix
Research and DevelopmentSpecific Cancer Marker Detection - The Underlying Technology (Add a write-up of the information discussed in Week 3's class) (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.)
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