Davidson Missouri W/Solving the HPP in vivo
From 2007.igem.org
m (typos) |
|||
| Line 3: | Line 3: | ||
<hr> | <hr> | ||
<br> | <br> | ||
| - | Using the Hin/'' | + | Using the Hin/''hixC'' flipping mechanism, we are developing a bacterial computer which solves a specific mathematical problem, the ''Hamiltonian Path'' problem. |
=The Hamiltonian Path Problem= | =The Hamiltonian Path Problem= | ||
| Line 11: | Line 11: | ||
==Designing a Plasmid== | ==Designing a Plasmid== | ||
| - | Our plasmid consists of reporter genes and '' | + | Our plasmid consists of reporter genes and ''hixC'' sites. ''hixC'' sites are placed within the coding regions of our reporter genes. The reporter genes are joined in such a way as to represent a graph. Each reporter gene represents a node, and the connection of two reporter genes together without any ''hixC'' sites in between represents an edge. |
[[Image:HamiltonianGraph.PNG|thumb|700px|center|Above: A graph on a plasmid. Below: flipping into a solution.]] | [[Image:HamiltonianGraph.PNG|thumb|700px|center|Above: A graph on a plasmid. Below: flipping into a solution.]] | ||
==Developing Nodes== | ==Developing Nodes== | ||
| - | We represent the graph's nodes with reporter genes. In order to allow for flipping, we must insert '' | + | We represent the graph's nodes with reporter genes. In order to allow for flipping, we must insert ''hixC'' sites within the coding regions of our reporter genes. We call this process [[Gene splitting|''gene splitting'']]. If our reporter gene tolerates a ''hixC'' insertion then we can use it as a node on our graph. |
Revision as of 20:14, 10 October 2007
Using the Hin/hixC flipping mechanism, we are developing a bacterial computer which solves a specific mathematical problem, the Hamiltonian Path problem.
The Hamiltonian Path Problem
A Hamiltonian Path is a trip through a graph which visits each node exactly once. A graph may have multiple Hamiltonian Paths, only one, or even none. Given a graph, a starting point and an endpoint, does it contain a Hamiltonian path?
We solve our problem by transforming E. coli cells with specially engineered plasmids.
Designing a Plasmid
Our plasmid consists of reporter genes and hixC sites. hixC sites are placed within the coding regions of our reporter genes. The reporter genes are joined in such a way as to represent a graph. Each reporter gene represents a node, and the connection of two reporter genes together without any hixC sites in between represents an edge.
Developing Nodes
We represent the graph's nodes with reporter genes. In order to allow for flipping, we must insert hixC sites within the coding regions of our reporter genes. We call this process gene splitting. If our reporter gene tolerates a hixC insertion then we can use it as a node on our graph.
