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Published byMelvin Richard Modified over 9 years ago
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Hamilton Path Problem Catherine Doyle, James Harden, Julia Fearrington
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Solving the Hamilton Path Problem Through Golden Gate Shuffling
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Golden Gate Shuffling vs. BioBricks Golden Gate Shuffling Pros – Allows us to split at any site with 4 bp in common – Hix sites unnecessary – No scars – Make all the edges possible – Make all possible paths – Feasible Selection processes – Quick1-2 hrs Cons – In vitro – More random assembly Bio Bricks Pros – Can flip single DNA fragment or multiple adjacent fragments – in vivo Cons – Scars – Takes a long time: days – Can only build one edge at a time – Attach each component through ligations – Unintentional recombination
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Design 6 Edges 6 Half edges RBS Promoter RBS A1 B1 C1 A2 C2 B2 Promoter B2 RBS A1 Promoter C2 Promoter A2 RBS B1 RBS C1
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Controlled Design PCR w/ primers to create 6 half edges Promoter B2 RBS A1 GGS RBS Promoter A1 B2 6X GGS N edges With all different half edges Size Selection Clone and Measure phenotypes Solution(s)
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1 st level of Randomness Design PCR w/ primers to create 6 half edges GGS RBS Promoter RBS A1 B1A2 C2 B2 Promoter RBS B1 C1 A2 C2 B2 Clone and PCR Screen for 6 desired edges Promoter RBS A1 B1 C1 A2 B2 C2 GGS N edges Size Selection Clone and Measure Phenotypes Solution(s) GGS N Edges Size Selection Clone and Measure Phenotypes Solution(s) OR Harder Problem Easier Problem
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2 nd Level of Randomness Design PCR w/ primers to create 6 half edges GGS N edges Size Selection Clone and Measure Phenotypes Solution(s)
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Column Method z z A1 X2 4 4 C1 X2 4 4 B1 X2 4 4 B1 A2 4 4 A1B2 4 4 B1C2 4 4 C1B2 4 4 C1A2 4 4 A1C2 4 4 A1B2 4 4 B1 C2 4 4 C1B2 4 4 C1A2 4 4 A1C2 4 4 B1A2 4 4 4 4 4 4 4 4 4 4 4 4 4 4 Y1A2 4 4 Y1 C2 4 4 Y1B2 4 4 4 4 4 4 4 4 4 4 4 4 4 4 GGS N Edges Clone and measure Phenotypes Solution(s) PCR w/ primers to create all half edges GGS
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Conclusions Can use GGS problems with Hin and Hix Probably will use the controlled method first go around and advance to the Column method. Using all 6 edges is not mathematically interesting but is biologically – Will probably not use all 6 edges in experiment
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