BME103:T130 Group 1 l2

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Owwnotebook icon.png BME 103 Fall 2012 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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Name: Tianzhu Zhu
Experimental protocol planner
Name: Wyatt Hansen
Open PCR machine engineer
Name: Bryce Hicok
Open PCR machine engineer
Name: Jesus Ibarra
Experimental protocol planner
Name: Emma Maiorella
R&D scientist


Thermal Cycler Engineering

Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.

System Design

PCR redesign.png
All wood structures will be replaced with a high density plastic material. The screws will be replaced with snap on hinges.

Key Features




Supplied in the Kit Amount
PCR Machine 1X
Sybr Green Buffer 1μL (Can be diluted up to 10,000 times)
Regular Buffer (Magnesium Chloride) 1μL (Can be diluted up to 10,000 times)
4 bases 25μL
Primers 25μL
Micropipets 4X
ImageJ Installation Disc 1X
DNA Polymerase 5,000 units/mL

Supplied by User Amount
DNA samples 1 pipet droplet

PCR Protocol

DNA Measurement Protocol

Research and Development

Background on Disease Markers

The disease marker being used is SNP (single nucleotide polymorphism) rs35685286. This is the marker for sickle-cell disease found on chromosome 11. Patients with sickle-cell disease have red blood cells that are mishapen and are a "sickled" or crescent shape. This results in less oxygen being carried to the patient's body tissues. Therefore, patients experience crisis, where they have severe pain in their bones in their backs or chest. These symptoms can last for hours or even days.

More information about this particular SNP can be found at:

Primer Design

The forward primer for this disease is ACTCCGGACCCGTCCAACCAT and the reverse primer for a patient without sickle-cell disease would be TGAGGCCTGGGCAGGGTTGGTA. If a patient were to be positive for sickle-cell disease, their reverse primer would be TGAGGCCTGGACAGGTTGGTA. Therefore, a patient with this disease experiences the gene mutation from G binding to C to G binding to A. A positive test will be recognizable because while the DNA is replicating during the PCR process, the reverse primers will only attach to the diseased patient's DNA. Consequently, when the reaction is complete and the SYBR green is added, the diseased patient's DNA will appear to glow green. If a patient does not have the disease, their DNA will be present in single strands and will appear clear when injected with SYBR green.


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