BME103:W930 Group4

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(Research and Development)
(Research and Development)
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'''Specific Cancer Marker Detection - The Underlying Technology'''<br>
'''Specific Cancer Marker Detection - The Underlying Technology'''<br>
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(What is the function of each component of a PCR reaction?
+
What is the function of each component of a PCR reaction?
 +
 
Template DNA:  
Template DNA:  
A double-stranded segment of DNA that encodes either a cancerous gene or a normal gene
A double-stranded segment of DNA that encodes either a cancerous gene or a normal gene
 +
Primers:
Primers:
Short segments of DNA that bind to a specific sequence of nucleotides (binds to cancer gene)
Short segments of DNA that bind to a specific sequence of nucleotides (binds to cancer gene)
 +
Taq Polymerase:
Taq Polymerase:
A protein that serves as the catalyst for the DNA replication; grabs extra nucleotides within the solution and binds them to the "unzipped" strands
A protein that serves as the catalyst for the DNA replication; grabs extra nucleotides within the solution and binds them to the "unzipped" strands
 +
Magnesium Chloride:
Magnesium Chloride:
A cofactor that binds to the Taq Polymerase and affects the speed of the reaction; positive correlation between amount of magnesium chloride and reaction speed
A cofactor that binds to the Taq Polymerase and affects the speed of the reaction; positive correlation between amount of magnesium chloride and reaction speed
 +
dNTP's:
dNTP's:
Deoxynucleotide triphosphates; extra nucleotide bases in solution that are able to be grabbed and synthesized by Taq Polymerase to replicate DNA strands beyond the primer sequence
Deoxynucleotide triphosphates; extra nucleotide bases in solution that are able to be grabbed and synthesized by Taq Polymerase to replicate DNA strands beyond the primer sequence
 +
What happens during each step of thermal cycling?
What happens during each step of thermal cycling?
 +
• At 95° Celsius: DNA melts and "unzips" to create two one-stranded strips, primers are added to the solution
• At 95° Celsius: DNA melts and "unzips" to create two one-stranded strips, primers are added to the solution
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• At 57°Celsius: Primers attach to the corresponding template sequence they complement, forming one forward primer and one reverse primer  
+
 
 +
• At 57°Celsius: Primers attach to the corresponding template sequence they complement, forming one forward primer and one reverse primer
 +
• At 72° Celsius: Taq Polymerase finishes the replication process with the use of dNTP's and magnesium chloride
• At 72° Celsius: Taq Polymerase finishes the replication process with the use of dNTP's and magnesium chloride
 +
 +
Why does a cancer gene produce a positive result while a normal gene produces a negative?
Why does a cancer gene produce a positive result while a normal gene produces a negative?
 +
• Because the cancer gene has the specific sequence of nucleotides that the primers can bond to, the process can continue and the DNA can be replicated; however, since the normal gene does not include that specific sequence, the primers can never bond to the strands and the process cannot take place.
• Because the cancer gene has the specific sequence of nucleotides that the primers can bond to, the process can continue and the DNA can be replicated; however, since the normal gene does not include that specific sequence, the primers can never bond to the strands and the process cannot take place.
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)<br>
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<br>
(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.)
(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.)

Revision as of 14:11, 31 October 2012

BME 103 Fall 2012 Home
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Lab Write-Up 1
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Contents

OUR TEAM

Name: Renaad AlawiRole(s)
Name: Renaad Alawi
Role(s)
Name: Lauren AllisonResearch and Development
Name: Lauren Allison
Research and Development
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(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)


Experimenting With the Connections

When we unplugged part (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

(Add your work from Week 3, Part 1 here)


Flourimeter Measurements

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




Research and Development

Specific Cancer Marker Detection - The Underlying Technology

What is the function of each component of a PCR reaction?

Template DNA: A double-stranded segment of DNA that encodes either a cancerous gene or a normal gene

Primers: Short segments of DNA that bind to a specific sequence of nucleotides (binds to cancer gene)

Taq Polymerase: A protein that serves as the catalyst for the DNA replication; grabs extra nucleotides within the solution and binds them to the "unzipped" strands

Magnesium Chloride: A cofactor that binds to the Taq Polymerase and affects the speed of the reaction; positive correlation between amount of magnesium chloride and reaction speed

dNTP's: Deoxynucleotide triphosphates; extra nucleotide bases in solution that are able to be grabbed and synthesized by Taq Polymerase to replicate DNA strands beyond the primer sequence

What happens during each step of thermal cycling?

• At 95° Celsius: DNA melts and "unzips" to create two one-stranded strips, primers are added to the solution

• At 57°Celsius: Primers attach to the corresponding template sequence they complement, forming one forward primer and one reverse primer

• At 72° Celsius: Taq Polymerase finishes the replication process with the use of dNTP's and magnesium chloride


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

• Because the cancer gene has the specific sequence of nucleotides that the primers can bond to, the process can continue and the DNA can be replicated; however, since the normal gene does not include that specific sequence, the primers can never bond to the strands and the process cannot take place.

(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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