Name: Adam Pak Role: Experimental Protocol Planner
Name: Sunshine Silvas Role: Machine Testing
Name: Renee Tran Role: Research and Development Scientist
LAB 1 WRITE-UP
Initial Machine Testing
The Original Design
(Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is)
The PCR Machine otherwise known as a Thermocycler or a DNA Amplifyer is use by scientists to create a vast quanity of a specific sequence of DNA. This method is also used widely for biological and medical applicaions. This process relies on the thermal cycles to amplify the DNA to then be able to replicated it. The system is run by means of a software downloaded to either a desktop or laptop. By connecting the PCR machine to a computer it is then possible to run a test with the unique specifications needed; such as tempurature and number of cycles.
Experimenting With The ConnectionsWhen taking apart the PCR Machine
Test Run
(Write the date you first tested Open PCR and your experience(s) with the machine)
Protocols
Experimental protocol planner summery
As experimental protocol planner we have taken on the challenge of making sure that the experiment goes as planned as well as the preparing software that was used to evaluate our samples. We have left the technical portions of experiments to our “Open PCR machine testers” and allowed our R&D scientists to educate us on our experiment so that we (Experimental protocol planners) could create a plan and execute it in order for the experiment as a whole to be successful.
Our job as for Experiment Protocol Planner was to :
Prepare the software for analysis
Prepare DNA samples for tests
Analyze the results
We have educated our self via “PCR Virtual Lab” that can be found at http://openpcr.ord/use-it/ then downloaded and test software that was responsible for taking the results from PCR machine and displaying those results on PC, as well as to make commends to the PCR machine. This software also gave us real time update of the PCR machine
Second and most important part of to prepare our sample. Our sample consisted of two rows of four samples. The table representing the samples is shown below. In this part we have also created a total of 8 different dyes also shown below.
The third part was to take the results from the PCR machine and analyze them with the rest of our team, via software. called
Thermal Cycler Program
PCR experiment summery
PCR machine goal is to take a long code of DNA and to amplify or separate a known part of that DNA. This target DNA is to be replicated with the help of PCR machine. We know which part of the DNA needs to be amplified because we know the sequence of bases of that particular part. We use the master mix which already contains the known sequence and will replicate only that known sequence leaving the the rest of the DNA. The PCR machine allows the master sample to perform its job by performing cycles of cooling and heating. The temperature changes allow different enzymes to perform their job in replicating the DNA. When the sample is heating the DNA opens up, the heat rises up to 95 degree Celsius. Then for primers to be allowed to do their job the sample is cooled down to 57 degree Celsius. Next for the primer to add appropriate amine acids in order to build a new DNA strand the sample is heated up to 72 degree Celsius. This sample is repeated multiple times allowing more and more replicates of the targeted DNA to be made, making the amount of the unwanted DNA to be minimal compared to the amount of wanted DNA.
DNA Sample Set-up
ID : 80175(1), 57483(2)
ROW :
Tube 1
Tube 2
Tube 3
Tube 4
Row 1
Contains : rep : Label
+ Control N/A "+"
- Control N/A "-"
Patient 1 1 "1"
Patient 2 1 "2"
Row 2
Contains : rep : Label
Patient 1 2 "+-"
Patient 2 2 "--"
Patient 1 3 "1-"
Patient 2 3 "2-"
"Contains" describes what sample was inserted in the test tube
"rep" is the replicate, we have 3 replicates of each patient
"label" is simply what symbol we have written on the test tube so that we can identify what sample is where
DNA Sample Set-up Procedure
1. Step 1 : Acquire Materials
Materials :
- A set of four dyes (blue, green, yellow, red)
- Sample containing (+,-,P1,P1,P1,P2,P2,P2)
- Pipette and tips
- two rows of empty test tubes
2. Step 2 : Mix dyes
MIX:
blue 50μL
blue 50μL
blue 50μL
yellow 50μL
blue 50μL
green 50μL
yellow 50μL
yellow 50μL
yellow 50μL
green 50μL
red 50μL
red 50μL
red 50μL
green 50μL
green 50μL
green 50μL
3. Step 3 : Prepare the samples, and label the samples (tables is shown above)
4. Step 4 : allow other team members to start PCR machine and then load the samples into the machine
5. Step 5 : Enter following commands to the Thermal Cycler Program so that the PCR machine knows what and how many cycle s to perform
Stage
Cycles
Heat (Celsius)
time
1
1
95
3 minutes
2
35
95 to 52 to 72
each 30 seconds
3
1
72
3 minutes
6. Step 6 : Start the PCR machine using software
PCR Reaction Mix
What is in the PCR reaction mix?
DNA/ primer mix
What is in the DNA/ primer mix?
Research and Development
Specific Cancer Marker Detection - The Underlying Technology
The goal of this experiment is to understand the DNA amplification process in order to detect cancerous genes when given Template DNA; otherwise known as DNA taken from the patient. DNA amplification will allow the cancerous genes to replicate. The cancerous gene will produce a positive result, while the non-cancer gene will give a negative result, because the primers are designed to amplify cancerous DNA. Therefore, the cancerous mutation cannot bind to normal DNA, ultimately meaning that amplification cannot occur.
Functions of each component of the PCR Chain Reaction: Template DNA: The DNA taken from the patient Primers: Short (20 base pairs) pieces of synthesized DNA Taq Polymerase: is an enzyme that detects the primer-template DNA and snaps the dNtp's back to DNA Magnesium Chloride (MgCl2): serves as a "co-factor" for Taq Polymerase dNTP's: Once the DNA is "unzipped"and recombined the dNTP's are the unincorporated bases
The following “3 steps” are repeated for 30 cycles, each step taking about 30 seconds.
Step 1:Heat up the Template DNA, Primers, Taq Polymerase, and Magnesium Chloride (MgCl2) to 95 degrees Celsius
• What happens?
o The bases need to me detected, in order to do so “melting” or unzipping needs to DNA will expose those base pairs.
o When the base pairs are exposed the primers will create a forward and reverse strand appropriately. The primers are short pieces (about 20 bases pairs long) of DNA that are synthesized DNA that binds to the Template DNA while directing the new strand to be made.
Step 2:The mixture is cooled down to 57 degrees Celsius
• What happens?
o The primers “anneal,” or in other words the bond.
Step 3:Heat the mixture back up to 72 degrees Celsius.
• What happens?
o The Taq Polymerase and Magnesium Chloride will detect where the template DNA and primer and uses the template DNA strand and primer to build a new copy of DNA
BME 103 Spring 2013
