BME103 s2013:T900 Group8

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(Research and Development)
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==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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''These “3 steps” are repeated for 30 cycles, each step taking about 30 seconds.''<br>
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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. 
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''The following “3 steps” are repeated for 30 cycles, each step taking about 30 seconds.''<br>
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'''Step 1:'''Heat up the Template DNA, Primers, Taq Polymerase, and Magnesium Chloride (MgCl2) to 95 degrees Celsius <br>
'''Step 1:'''Heat up the Template DNA, Primers, Taq Polymerase, and Magnesium Chloride (MgCl2) to 95 degrees Celsius <br>
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• What happens? <br>
• What happens? <br>
o The bases need to me detected, in order to do so “melting” or unzipping needs to DNA will expose those base pairs.
o The bases need to me detected, in order to do so “melting” or unzipping needs to DNA will expose those base pairs.
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o When the base pairs are exposed the primers will create a forward and reverse strand appropriately
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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.
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'''Step 2:'''The mixture is cooled down to 57 degrees Celsius<br>
'''Step 2:'''The mixture is cooled down to 57 degrees Celsius<br>
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• What happens?<br>
• What happens?<br>
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o The Taq Polymerase detect where the template DNA and primer and uses the template DNA strand and primer to build a new copy of DNA
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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<br>
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*Remember: The cancer 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. *
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Revision as of 20:25, 23 March 2013

BME 103 Fall 2012 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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Contents

OUR TEAM

Name: studentRole(s)
Name: student
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Name: student
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Name: studentRole(s)
Name: student
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Name: student
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Name: student
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Name: Renee TranRole: Research and Development Scientist
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)


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

Thermal Cycler Program

DNA Sample Set-up

row 1 cell 1 row 1 cell 2 row 1 cell 3 row 1 cell 4
row 2 cell 1 row 2 cell 2 row 2 cell 3 row 2 cell 4

DNA Sample Set-up Procedure

  1. Step 1
  2. Step 2
  3. Step 3...

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.

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


Cancer Associated with the gene:
Chromosome:
Gene being analyzed:
SNP #:
SNP's Surrounding DNA:
Cancer-Sequence Primer:
"Partner Primer":
Description of Gene:

(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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