Difference between revisions of "Team:UMaryland/Description"

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<a href ="#What is PCR" class = "container btn btn-primary btn-lg col-xs-10 col-xs-offset-1  col-sm-2 col-sm-offset-1">What is PCR</a>
 
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<h1> What is PCR </h1>
 
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Polymerase Chain Reaction or PCR is a common tool used in the field of biology to amplify DNA or RNA. Invented by Dr. Kary Mullis, PCR is conducted trough cycling DNA, primers and enzyme through various temperatures. Generally starting with a value near and above 90 degrees Celsius; used to break the Hydrogen bonds between double strands a process called denaturation. The machine then cools down to annealing temperature, with values near 50-60 degrees, at this point primers are able to attach to the template strand of DNA. This stage is then followed by extension temperature, around 72 degrees, at this point the polymerase is able to extend and add nucleotides to the primer.
 
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<h1>Thermocycler </h1>
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<h1> Purpose </h1>
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Although the process of amplifying genetic material is remarkable, the hardware needed to do it is relatively simple-- all that is required are three different temperatures which are maintained by the machine, enabling the enzymes and template to do the work of PCR. Current PCR machines cost thousands of dollars, and although there exists open source, DIY PCR machines, their costs still range in the hundreds of dollars. Here at the University of Maryland, we thought that that was an absurd notion. PCR, because of its simplicity and utility, is a robust tool for the diagnosis of many diseases both in the developed and developing world. Making the device cheaper would give more people accessibility to this platform. Accessibility enables further innovation and development of novel methods for disease detection and this in turn enables better and faster diagnosis and treatment both in the developed and developing world.  
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PCR is often a common tool in the laboratory environment. It is also a vital component in DNA amplification and any cloning procedure. However the majority of theses devices are bulky expensive machines that are rarely seen outside of bio based labs. This was the premise for the development of CHIP or Cheap Homemade Innovative PCR, development of a compact PCR machine that was as fast and proficient at amplifying DNA as lab based machines but for the fraction of the price and for teaching based applications. We are proud to say that we have been able to design a machine that will be completely open source and able to serve as a platform for DIY cloning procedures.                
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Another major advantage of "cheap" is education. Here at the University of Maryland, we acknowledge that iGEM is a competition, however we also understand that this competition is also a collaboration. It is an opportunity for all of us to learn from one another and serves as the foundation for future discovery, innovation, and new projects. We hope that our work with the PCR machine will inspire many more teams to tackle designing hardware. We hope that our current collaborations with Duke University foster better and more innovative projects from both of our teams. And most important, we hope that our efforts will be able to inspire the future generation of iGEMer's and the newest members of the iGEM community; high school students.
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I remember, along with my fellow teammates, learning about PCR by cutting up little paper nucleotides and putting them into a brown bag and then having our hands act as the "polymerase" that would pluck the nucleotides out and match them with the template strand we were given. I remember taking away very little from this "lab" other than a few paper cuts. In subsequent years, I went through a few internship programs where I was able to learn in greater detail the steps of PCR, eventually learning how to design primers, program the machine, and setup my own reactions. However, I believe that if we truly want to bring synthetic biology to the public, we have to allow them the opportunity to actually do PCR, not through a paper bag which is conceptual understanding, but a real reaction where the end products are the real deal, actual amplified DNA. We still have a ways to go... the enzymes have to become cheaper pipettes need to become cheaper, but designing a below 50 dollar PCR machine is the first step in this endeavor.                  
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<p>CHIP1 is our first design and employs, in many respects, a more conventional PCR design. CHIP1 utilizes two peltier units below an aluminium heating block to heat the PCR tubes sitting inside the block. We use a temperature sensor to detect the temperature of the wells in which the PCR tubes are housed. The sensor then reports back to the Arduino unit, which regulates the energy flow to the peltier units, thereby heating and cooling the block and the tubes.</p>
 
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<p>CHIP2, our second thermocycler, is mostly made out of a salvaged hairdryer
 
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Revision as of 16:13, 1 September 2015