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Team:Alberta
From 2009.igem.org
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BioBytesSynthetic biology needs more than minor modifications to existing evolutionary plans. We’ve developed a method allowing complete genome re-design, based on artificial design principles such as maximizing modularity by grouping common pathway components and components with similar levels of expression. This degree of organism control would be a milestone marking Synthetic Biology as a mature field. Genome design and reconstruction would allow us to rapidly test, optimize and correct design principles on a simple chassis that could be reliably modeled. There are currently two alternatives for gene assembly. The first, BioBricks, is modular but slow. The second, the use of unique long sticky ends for each piece, is fast but non-modular. BioBytes is the only method that is fast, modular, sequential and in vitro:Fast: The addition of each DNA segment takes only 20min, a roughly 200-fold increase in speed from traditional cloning. Moreover, we’ve demonstrated that the Biobytes method works on microfluidic chips and is automatable both on lab-bench and microfluidic scales. Modular: this allows standard parts such as the backbone primers and USER primers to be reused, greatly reducing expenses for large scale projects. Once parts are in pAB or pBA, they can be rapidly assembled in any order, allowing easy testing of alternative designs. Sequential: Biobytes allows tight control over the order of gene assembly. New DNA segments can add only to the unanchored end, and only with their complementary end. Using two different sets of complementary ends prevents concatamerization of parts before assembly. In vitro: Using an organism as an intermediate is time-consuming and limits one’s ability to control and assess the changes that it is making. With current advances in transformation, genome-sized constructs assembled in vitro can later be transformed into an organism. Biobytes allows the in vitro assembly. Overall, the BioBytes method gives synthetic biology the tools to understand and organize complexity, standardize robust parts, use modular strategies and rapidly test rational designs and computational models. With BioBytes we can start asking the most fundamental questions - To what extent do the rules of engineering hold true for biology? To what degree does life equal the sum of its parts? The BioBytes gene assembly method can be applied to numerous different applications, however, its greatest application is for the assembling of entire genomes. For this reason we have provided a detailed explanation regarding the requirements of constructing a minimal genome including an in-silico method for identifying essential genes in any organism, and a theoretical design of replacing the host chromosome with the new synthetic genome. |
The Minimal Genome ProjectThe minimal Escherichia coli genome has been the holy grail of biology for a number of years. E. coli is the most widely used cellular research tool by the molecular biology community. Since scientific research is based upon reductionism and simplification for understanding, a simplified version of an experimental model organism such as E. coli is ideally preferred as a chassis for experimentation. Reducing the E. coli genome to roughly 10% of its original size, demonstrates a great simplification of this model organism. To reconstruct such an organism, we plan on building an artificial E. coli chromosome using the BioBytes chromosome assembly system and inserting it into living E. coli cells. At the same time, the original host chromosome is displaced, effectively rebooting an E.coli cell with the synthetic chromosome. This is markedly different from the current, time-consuming method of knocking out inessential genes, one at a time, in an effort to produce the minimal genome. It is this difference that we hope to exploit in our attempt to win the race to produce the ideal model organism |
Team AchievementsThrough our efforts we have made the following accomplishments:
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