We introduce programmed mutagenesis, a technique for rewriting DNA strands according to programmed rules. We present the Unary Counter-a simple computational system based on programmed mutagenesis.We present the experimental results of the first two cycles of the unary counter which show that string rewriting by programmed mutagenesis is possible. We discuss the two enzyme system which allows to implement programmed mutagenesis by thermocycling a single reaction in a single test tube.We discuss the sources of rewrite rule specificity within the framework of programmed mutagenesis and present experimental results which indicate that it is possible to guarantee the specificity of the rewrite rules, and thus the correctness of the computation.We demonstrate that two oligonucleotides annealing to the template next to each other can ligate and extend to form the correct product. We argue that the ability to have oligonucleotides in close proximity function properly, together with the MIMD nature of the programmed mutagenesis systems provides evidence that parallel and nondeterministic computations are possible with programmed mutagenesis.Finally, we discuss the significance of our results and outline directions for future work.
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