Difference between revisions of "Team:UMaryland/Hardware"

Revision as of 20:14, 24 August 2015

UMD PCR

What is PCR

Purpose

CHIP

What is PCR

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.

Purpose

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.

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.

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.

Cheap Homemade Innovative PCR

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.

CHIP2, our second thermocycler, is mostly made out of a salvaged hairdryer

Design of THING2

The design of THING2 started when we bought a hairdryer in the hopes of using the heating unit as part of our first PCR machine. However, as we were dismantling and testing the hairdryer, it became apparent to us that the heating system inside the hairdryer could reach the necessary temperatures independent of the peltier units already in use. With this in mind, we began working out how to wire the hairdryer so that we could regulate the heating unit and the fan separately.

After a lot of soldering and some potential fires, we were able to wire the system so that we could turn the heat on and off while running the fan continuously. Using autoclave tape, we secured a sheet of aluminium foil to the top of the heating unit of the hairdryer. The outer casing of the hairdryer had been removed. We placed a heat sensor inside the tin to measure the temperature of the air inside the machine. By wiring the heat sensor to the arduino controlling the heat unit, we were able to regulate the heat of the machine. THING2 now thermocycled.

At this point, we tried to perform our first PCR reaction, but the PCR tube melted. We learned that we needed to modify the code to prevent an overshoot of the highest temperature. We did so, but the PCR still failed. Attempting to solve this issue, we drilled equally spaced holes in a coke can, which we fashioned to the top of the heating unit using aluminum tape and autoclave tape. We placed the heat sensor in one of these holes and tried again to perform a PCR reaction and again failed. Assuming the temperatures inside the machine were passing 100 degrees Celsius, we put the heat sensor inside a PCR tube with mineral oil and placed this inside one of the holes. We ran another PCR reaction, performed a PCR clean-up, ran the products on a gel and saw a large band of the correct size, indicating that THING2 works.

@@ Line 93: / Line 93: @@
 <br>
 <p>CHIP2, our second thermocycler, is mostly made out of a salvaged hairdryer
+<div style="clear:both">
+<a name = "Design2">
+<h1> Design of THING2</h1>
+</a>
+<p>The design of THING2 started when we bought a hairdryer in the hopes of using the heating unit as part of our first PCR machine. However, as we were dismantling and testing the hairdryer, it became apparent to us that the heating system inside the hairdryer could reach the necessary temperatures independent of the peltier units already in use. With this in mind, we began working out how to wire the hairdryer so that we could regulate the heating unit and the fan separately.
+<br></br>
+After a lot of soldering and some potential fires, we were able to wire the system so that we could turn the heat on and off while running the fan continuously. Using autoclave tape, we secured a sheet of aluminium foil to the top of the heating unit of the hairdryer. The outer casing of the hairdryer had been removed. We placed a heat sensor inside the tin to measure the temperature of the air inside the machine.  By wiring the heat sensor to the arduino controlling the heat unit, we were able to regulate the heat of the machine. THING2 now thermocycled.
+<br></br>
+At this point, we tried to perform our first PCR reaction, but the PCR tube melted. We learned that we needed to modify the code to prevent an overshoot of the highest temperature. We did so, but the PCR still failed. Attempting to solve this issue, we drilled equally spaced holes in a coke can, which we fashioned to the top of the heating unit using aluminum tape and autoclave tape. We placed the heat sensor in one of these holes and tried again to perform a PCR reaction and again failed. Assuming the temperatures inside the machine were passing 100 degrees Celsius, we put the heat sensor inside a PCR tube with mineral oil and placed this inside one of the holes. We ran another PCR reaction, performed a PCR clean-up, ran the products on a gel and saw a large band of the correct size, indicating that THING2 works.
 </div>