This web page was produced as an assignment for an undergraduate course at Davidson College.
Multiple pancakes and one-time HixC sites in E. coli computers
Karen Acker1, Bruce Henschen1, Karmella Haynes1 (mentor), Laurie J. Heyer2 (mentor), and A. Malcolm Campbell1 (mentor)
1Biology and 2Mathematics Departments, Davidson College, Davidson, North Carolina;
In the field of synthetic biology, E. coli can act as a biological computer to compute solutions to mathematical problems. Our lab has focused on the ‘Burnt Pancake Problem,’ a puzzle involving a series of scrambled pancakes that are burnt on one side and must be assorted in the correct order (biggest to smallest) and orientation (burnt side down). We have genetically mimicked the pancake scenario by building Biobrick constructs with DNA ‘pancakes’ and Hin protein ‘spatulas’ that recognize DNA flanked by HixC sites. Using a promoter and TetA(C), we have built two-pancake stacks. We are currently investigating the possibility of inserting HixC sites within the DNA sequence of GFP and TetA(C). As opposed to flanking genes with HixC sites, inserting HixC sites within a gene sequence increases the number of pancakes in a stack without increasing the number of genes. We also attempted to design and build mutant Hix sites that would permit intervening DNA segments to be flipped only once, providing greater Hin flipping control. Sites were designed and paired with wild-type Hix sites to determine functionality. A screen was designed to test whether paired Hix mutants can create Hix sites that allow only one DNA flipping event.
Splitting genes to make multiple pancakes
One-time flippable HixC sites
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