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Karmella A Haynes¹, Marian L Broderick, Adam D Brown

¹Davidson College, Department of Biology, Davidson, NC 28036, USA. karmella@gmail.com.

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|May 22, 2008

Summary

This summary is machine-generated.

Researchers engineered E. coli for DNA-based computation, solving the Burnt Pancake Problem using a novel Hin/hix DNA recombinase system. This system demonstrates in vivo DNA segment sorting via inversions, paving the way for complex genetic manipulations.

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Area of Science:

Synthetic Biology
Computational Biology
Molecular Biology

Background:

Investigated DNA-based computation within living cells.
Engineered Escherichia coli to solve the Burnt Pancake Problem (BPP).
BPP involves sorting objects (pancakes) using minimal reversals.

Purpose of the Study:

To demonstrate DNA-based computation in vivo.
To utilize site-specific DNA recombination for genetic element manipulation.
To engineer a system for solving the Burnt Pancake Problem in E. coli.

Main Methods:

Designed a system using Salmonella typhimurium Hin/hix DNA recombinase.
Reconstituted modular genetic elements for use in E. coli.
Mediated inversions of DNA fragments representing pancakes within plasmid DNA.

Main Results:

Successfully sorted DNA segments via inversions, creating permutations of promoter and tetracycline resistance regions.
E. coli exhibited antibiotic resistance upon proper sorting of DNA segments.
Hin recombinase mediated all possible inversion operations on adjacent DNA fragments.
In vivo flipping occurred over hours or days, as indicated by semiquantitative PCR.

Conclusions:

The Hin/hix system serves as a proof-of-concept for in vivo computation.
This system has potential for scaling to larger, more complex computational problems.
Hin/hix offers a novel tool for in vivo manipulation of transgenic DNA.