DNA-Templated Synthesis Optimization.

Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, and Alexei Mihalchuk.
In 23rd International Conference on DNA Computing and Molecular Programming (DNA), volume 10467 of Lecture Notes in Computer Science, pages 17-32. Springer, 2017.

In chemistry, synthesis is the process in which a target compound is produced in a step-wise manner from given base compounds. A recent, promising approach for carrying out these reactions is DNA-templated synthesis, since, as opposed to more traditional methods, this approach leads to a much higher effective molarity and makes much desired one-pot synthesis possible. With this method, compounds are tagged with DNA sequences and reactions can be controlled by bringing two compounds together via their tags. This leads to new cost optimization problems of minimizing the number of different tags or strands to be used under various conditions. We identify relevant optimization criteria, provide the first computational approach to automatically inferring DNA-templated programs, and obtain optimal and near-optimal results.

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