BME103:W930 Group4

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Initial Machine Testing)
(Research and Development)
Line 97: Line 97:
<br>
<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.)
+
[[Image:Target.PNG]]
 +
[[Image:Primer.PNG]]
 +
[[Image:Polymerase.PNG]]
 +
[[Image:Two_Strands.PNG]]
 +
Image Credit to OpenPCR.org/use-it/
<br><br>
<br><br>

Revision as of 13:29, 31 October 2012

BME 103 Fall 2012 Home
People
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Photos
Wiki Editing Help
Image:BME494_Asu_logo.png

Contents

OUR TEAM

Name: Renaad AlawiExperiemental Protocol Planner
Name: Renaad Alawi
Experiemental Protocol Planner
Name: Lauren AllisonResearch and Development
Name: Lauren Allison
Research and Development
Name: Jake KrammerOpen PCR Machine
Name: Jake Krammer
Open PCR Machine
Name: Jan SimperOpen PCR Machine
Name: Jan Simper
Open PCR Machine
Name: Justus VangroResearch and Development
Name: Justus Vangro
Research and Development
Name: Christian VargasExperimental Protocol Planner
Name: Christian Vargas
Experimental Protocol Planner

LAB 1 WRITE-UP

(Please finish by 11/7/2012)

Initial Machine Testing

The Original Design
Image:PCR machine.png The Polymerase Chain Reaction(PCR) machine essentially tests sequences of DNA for variations in nucleotides. This simple device is portable, easy to use, and relatively inexpensive. It is able to test up to 16 samples of DNA at a time and can be connected to a computer for ease of use. The machine heats up DNA samples so the samples disassociate allowing a primer to connect to the sequences of DNA and then the machine cools the DNA samples down with the primer in place.

Experimenting With the Connections

When we unplugged the mounting plate from the circuit board, the machine the LCD light and the menu on the PCR machine shut off.

When we unplugged the white wire that connects the circuit board to PCR block that holds the samples, the temperature on the menu on the PCR machine dropped from room temperature to -40.0 degrees Celsius. The white wire is the temperature sensor wire.


Test Run

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




Protocols

Polymerase Chain Reaction

(The Polymerase Chain Reaction works by)


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.

Image:Target.PNG Image:Primer.PNG Image:Polymerase.PNG Image:Two_Strands.PNG

Image Credit to OpenPCR.org/use-it/



Results

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


Personal tools