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Revision as of 23:39, 13 October 2010
Project Overview
Genomikon: an Educational Toolkit for the Rapid Assembly of Plasmids
Synthetic biology is a new and expanding field that has potential applications in every aspect of society. Today, synthetic biology is underused because it is expensive and slow. The University of Alberta is developing a method of plasmid assembly that is modular, rapid, and inexpensive. We are in process of designing an educational kit, Genomikon, which will enable anyone to construct a plasmid without special equipment. We will also provide a comprehensive lab manual to accomodate those new to the field.
To demonstrate the accessibility of our Genomikon toolkit, we will implement it in a high school laboratory setting. Genetic parts will be adapted into a system called BioBytes. This system will allow students to rationally create functional plasmids. The kit’s flexiblity will accomodate both predesigned experiments and new creative expressions. We believe that our kit could revolutionize science education. Our project not only seeks to optimize current procedures of synthetic biology but will also expose a new generation of students to this exciting field.
BioByte Theory
The DNA components of the Genomikon kit will be provided in linear pieces named BioBytes. These Bytes have 4 base 5' overhangs on both ends which gives specificity to the bytes that can neighbor it. BioBytes come in two flavors: A bytes and B bytes, which are defined by the composition of the overhangs it has. The result is that A bytes can only be ligated to B bytes and vise versa leading to a construct alternating in A and B bytes. The specificity in absolute order of a construct is given by an anchor which restricts ligation to only one side. File:D/dc/Alberta2010kaTheoryimage.jpg
The Genomikon Kit
The GENOMIKON kit was designed for a high school environment. The major challenge then facing the GENOMIKON kit was that high schools lack lab most equipment traditionally needed for molecular biology experiments. Further creating a sterile environment to avoid contamination was another challenge that had to be overcome. Fortunately the biobyte assembly method does not require centrifuges, thermocyclers or extreme accuracy with regards to volume and temperature. The only equipment a high school must supply then is a hot plate thermometer and a beaker. The issue of sterility is addressed by sending all the parts necessary to be sterile in sterilized packages. The kit sends everything that a high school would need to perform the transformations using synthetic parts.
Genomikon Online
For the GENOMIKON kit to be functional students and teachers need access to a lab manual that can accommodate the many different experiments possible. The GENOMIKON lab manual was designed to act as a teaching resource giving students background information for the experiments they design. GENOMIKON ONLINE was created as the lab manual complementary to the GENOMIKON kit. GENOMIKON ONLINE is found at the website www.genomikon.com. Features include: descriptions of the different parts used to construct a plasmid, a sandbox were student’s engineer their own unique experiments by dragging and dropping different parts into sequence automatically generating a protocol to follow. Students can also do predetermined experiments outlined and collect background information reading articles. Lastly the teacher can coordinate the class experiments by working through the groups feature.
Plates
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Software
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