BME103:T930 Group 6

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Contents

OUR TEAM

Name: Nicholas SterkowitzOpen PCR machine engineer
Name: Nicholas Sterkowitz
Open PCR machine engineer
Name: Dominic IlardiOpen PCR machine engineer
Name: Dominic Ilardi
Open PCR machine engineer
Name: Alexandra NazarenoExperimental Protocol Planner
Name: Alexandra Nazareno
Experimental Protocol Planner
Name: Amanda SweigExperimental Protocol Planner
Name: Amanda Sweig
Experimental Protocol Planner
Name: Taylor DeeganResearch and Development(s)
Name: Taylor Deegan
Research and Development(s)

LAB 1 WRITE-UP

(Please finish by 11/7/2012)

Initial Machine Testing

The Original Design
(Add image of the full OpenPCR machine here, from the Week 3 exercise. Write a paragraph description for visitors who have no idea what this is)

Open PCR
Open PCR
]

Experimenting With the Connections

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)


Test Run

(Write the date you first tested Open PCR and your experience(s) with the machine)




Protocols

Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is a biochemical process the replicates and amplifies a desired sequence of DNA. The original DNA strand is pulled apart and primer marks the location of the targeted DNA sequence for polymerase to begin replication of the complementary strands. This process is continued until there are an exponentially increasing amount of the desired strand, allowing it to be closely examined.The PCR reaction relies on thermal cycling, in which repeated cycles of cooling and heating the samples enable the enzymes to appropriately replicate the targeted strand, and carry out the processes previously described.

The Steps:

1. Obtain DNA sample and label them clearly.

2. Using a micro-pipette, transfer the proper amounts of forward primers, reverse primers, dNtP's and Taq Polymerase master mix to each the 8 labeled DNA sample tubes. Be sure to replace the pipette tip after every transfer to avoid contamination.

3. Place the DNA sample tubes into the Open PCR machine.

4. Close lid and tighten screw until it touches the tops of the tubes.

5. Program the machine to run the following cycles:

- Stage 1: 1 cycle, 95 degrees Celsius for 3 minutes

- Stage 2: 30 cycles, 95 degrees for 30 seconds, 57 degrees for 30 seconds, 72 degrees for 30 second

- Stage 3: 72 degrees for 3 minutes

- Final Hold: 4 degrees


PCR Master Mix Components

GoTaq® DNA Polymerase is supplied in 2X Colorless GoTaq® Reaction Buffer (pH 8.5), 400μM dATP, 400μM dGTP, 400μM dCTP, 400μM dTTP and 3mM MgCl2.


Reagent Volume
Temple DNA (20 ng) 0.2 μL
10 μM forward primer 1.0 μL
10 μM reverse primer 1.0 μL
GoTaq master mix 50.0 μL
dH2O 47.8 μL
Total Volume 100.0 μL

Patient Information

The eight samples that were tested consisted of a positive and negative control. The other six had three DNA samples from one patient and three DNA samples from the second patient. The first patient has an ID of 51919, and is a female that is fifty-four years of age. The second patient has an ID of 60627, and is also a female, but with an age of sixty-three.

Flourimeter Measurements

Flourimeter Assembly Procedure

1. Remove lid from black box and invert the box, open the front flap.

2. Place glass slide into holder.

3. Using pipette, squeeze two drops of SYBER green dye along the round glass windows on slide.

4. Add DNA sample to dye.

5. Move holder apparatus inside the box so that no light reaches it.

6. Place smartphone onto holder and direct camera lens at the slide apparatus..


ImageJ Procedure (Add your work from Week 3, Part 2 here)




Research and Development

Specific Cancer Marker Detection - The Underlying Technology

Polymerace chain reaction (PCR) is a biochemical technology that is used to amplify a specific piece of DNA by generating thousands to millions of copies of a particular DNA sequence. The method relies on thermal cycling by heating and cooling the DNA so that the double strands break apart and can be replicated.

What are the component of a PCR reaction?

Template DNA: A specific DNA sequence that is trying to be detected.

Primers: A short segment of DNA sequences that is complementary to the target DNA sequence and binds to the targeted nucleotides.

Taq Polymerase: An enzyme that is active at high temperature that begins at the primer and takes complementary nucleotides from the solution and binds them to the "unzipped" strands.

Magnesium Chloride: A cofactoe that attaches to the Taq Polymerase to affect the speed of the reaction.

dNTP's: Deoxynucleotide triphosphates; individual nucleotide bases in that solution that are attached to the replicated DNA strands by Taq Polymerase.

What happens during each step of the thermal cycle?

  • At 95° Celsius: The DNA double helix "unzips" to reveal two complementary single strands.
  • At 57° Celsius: Primers attach to the complementary template sequence forming one forward and one reverse primer.
  • At 72° Celsius: Taq Polymerase starts at the primer and replicates a complementary strand of DNA using the individual nucleotide bases in the solution.

The r17879961 cancer-associated sequence begining tested for is AAACTCTTACACTGCATACA. The bolded C represents the cancer gene that appears because the C took the place of the normal T that should be present. The one nucleotide base that was changed results in producing the amino acid of threonine instead of isoleucine. Because of the change in the amino acid begin produced, a study in Finland has found that this sequence has been link to susceptibility to colorectal cancer. Of the patients tested, 7.8% of the patients with colorectal cancer had the allele while 5.3% of patients without colorectal cancer had the same allele.

Why does a cancer gene produce a positive result while a normal gene produces a negative?

  • Since the primer is purposely selected to bind to the specific sequence of nucleotides that makes up the cancer gene, if the cancer gene is not present in the DNA, then the primers will not attach to the seperated DNA strands and replication will not take place, resulting in a negative result. However, if the cancer gene is present then the primers will attach and Taq Polymerase will begin the replication creating an exponential copies of the desired gene resulting in a positive result.

Relation to Bayers' Rule: Bayers' rule is used to determine the probability of true positives, false positives, and false negatives to predict the reliability of the process in detecting the cancer sequence in patients.


(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.)




Results

(Your group will add the results of your Fluorimeter measurements from Week 4 here)


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