DAN-based string rewrite computational systems

We describe a DNA computing system called programmed mutagenesis. prove that it is universal, and present experimental results from a prototype computation. DNA is a material with important characteristics, such as possessing all the information necessary for self-reproduction in the presence of appropriate enzymes and components, simple natural evolution mechanism, and miniature scale, all of which make it an attractive substrate for computation. For computer science, using single DNA molecules to represent the state of a computation holds the promise of a new paradigm of composable molecular computing. For biology, the demonstration that DNA sequences could guide their own evolution under computational rules may have implications as we begin to unravel the mysteries of genome encoding. Programmed mutagenesis is a DNA computing system that uses cycles of DNA annealing, ligation, and polymerization to implement programmatic rewriting of DNA sequences. We report that programmed mutagenesis is theoretically universal by showing how Minsky's 4-symbol 7-state Universal Turing Machine can be implemented using a programmed mutagenesis system. Each step of the Universal Turing Machine is implemented by four cycles of programmed mutagenesis, and progress is guaranteed by the use of alternate sense strands for each rewriting cycle. We constructed a unary counter, an example programmed mutagenesis system, and operated it through three cycles of mutagenesis to gather efficiency data. We showed that the counter operates with increasing efficiency, but decreasing overall yield.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2002

Author dc:creator

• Khodor, Julia, 1974-

Advisor dc:contributor.advisor

• David K. Gifford.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/8339

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/8339