Difference between revisions of "Team:UMaryland/Design"

Revision as of 21:54, 18 September 2015

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UMD DIY PCR

How we created a dual purpose PCR machine and incubator out of a hair dryer.

Background

The PCR machine is a common machine used in biological laboratories to amplify or extend fragments of DNA to be used in subsequent experiments. This tool is especially relevant to iGEM and SynBio labs who pave the way to vaster applications of We began this project with the vision to create a machine that would be

Our first design for a DIY PCR machine was modeled after a more conventional PCR machine. This first prototype relied on two Peltier units stacked on top of each other to heat a customized aluminum block that held the PCR tubes. In order for the system to have feedback, we embedded a temperature sensor in the aluminum block to measure the temperature of the PCR tube wells. The sensor then reported back to an Arduino UNO, which then regulated the energy flow to the Peltier units, thereby regulating the temperature of the block and tubes. However, after much testing, this design proved to be unoriginal, expensive, and inefficient. While the conventionality of the design itself did not pose an issue, we realized that the parts used to assemble it were not as well-known or easily accessible to the general public, which we felt would take away from the possible applications of this machine. In addition, although the price of this first prototype was relatively inexpensive in contrast to laboratory grade PCR machines, the price still ranged in the hundreds of dollars. Finally, the greatest issue with our design was the inefficiency of the hardware; we found that the Peltier units were not able to quickly cycle through the desired temperatures, causing the unit to take 5 to 10 minutes just to rise up to 95℃. After considering all of these factors, we began a redesign of our machine to better suit the needs of the DIY market.

The idea for our current thermocycler design first came into form when we found that our original prototype was not ramping up to the desired temperatures fast enough. We thus looked into other options such as the heating element in a hair dryer. We found that the hair dryer was able to reach very high temperatures—much higher than the desired maximum of 95℃ for PCR—in a matter of seconds. We then made a decision to suspend construction on the Peltier-centered thermocycler in order to see how successful we could be with making a rapid PCR machine out of a hair dryer. Before this decision, we took into consideration the danger of working with a hair dryer, failure due to uncertainty that the machine could be effectively controlled, and, on top of that, having less time to work on it. Nevertheless, we took the risk.
Please continue on to see the design of our machine.

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 polymerase through various temperatures. The reaction is started by heating the reaction mix to 95 degrees Celsius. The high heat overcomes base stacking interactions and hydrogen bonds which maintain the double helix, a process called denaturation. The machine then cools down to an annealing temperature in order for primers, short ssDNA oligos, to recognize selected DNA sequences, form duplex, and allow for polymerase to bind. Annealing is followed by extension, which is performed by the polymerase at its active temperature, typically around 72 degrees. The polymerase forms a daughter strand by adding nucleotides to the primer in the 5'-3' direction. I don't think this is necessary, especially not here. If you want to write how PCR works, put it in description. PCR is also a very complicated process so we'll need to invest a lot of space into it if you want to do it justice

Construction Hazard. Build at your own risk.

UMD DIY PCR

Our first design for a DIY PCR machine was modeled after a more conventional PCR machine design. This first prototype consisted of two Peltier units stacked on top of each other that would then heat a customized aluminum block that sat on top of the two units and held the PCR tubes. In order for the system to have feedback, we embedded a temperature sensor in the aluminum block to measure the temperature of the PCR tube wells. The sensor then reported back to an Arduino UNO, which then regulated the energy flow to the Peltier units, thereby regulating the temperature of the block and tubes. However, after much testing, this design proved to be unoriginal, expensive, and inefficient. While the conventionality of the design itself did not pose an issue, we realized that the parts used to assemble it were not as well-known or easily accessible to the general public, which we felt would take away from the possible applications of this machine. In addition, although the price of this first prototype was relatively inexpensive in contrast to laboratory grade PCR machines, the price still ranged in the hundreds of dollars. Finally, the greatest issue with our design was the inefficiency of the hardware; we found that the Peltier units were not able to quickly cycle through the desired temperatures, causing the unit to take 5 to 10 minutes just to rise up to 95℃. After considering all of these factors, we began a redesign of our machine to better suit the needs of the DIY market.

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 <p> We have had one successful amplification with our machine however we understand that repeatability is a vital component of all lab work and currently we are attempting to make our device repeatable. From our early days of testing we found that peltier units were not powerful enough to enable PCR tube to reach 95 degrees. <strike>Although conventional PCR machines use these units frequently they are often specialized and tailored made to perform PCR. With this tailoring comes a high price tag that does not suit the DIY market, and so we found a solution in the form of a hairdryer. </strike><b>On the other hand, t</b>he fan and heating element of a <b>cheap </b>hairdryer provide a control scheme that enables for <b>rapid</b> cycling of temperature<strike> rapidly and accurately and they are relatively inexpensive</strike>. We have found that developing a housing for the PCR tubes and enabling even heat distribution is challenging. We often have found that our temperature sensor and the pcr reaction tube are not at the same temperature and degree of difference is a delta of over 10 degrees celsius<b>It is therefore NOT accurate, as described in previous sentences</b>. We are currently working of milling a block of aluminum with better and more consistent heat transfer properties, and modeling the heat transfer within the can. Our ambition is that this will enable better control of temperature within the device.
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 <font color="#000000">#include</font> <font color="#434f54">&lt;</font><font color="#000000">PID_v1</font><font color="#434f54">.</font><font color="#000000">h</font><font color="#434f54">&gt;</font>

Difference between revisions of "Team:UMaryland/Design"

Revision as of 21:54, 18 September 2015

Warning banner up here

UMD DIY PCR

Background

What is PCR?

UMD DIY PCR

Design

Hardware

Problems and Current issues

CODE