DNA-templated synthesis optimization

Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle*, Alexei Mihalchuk

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

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 (sequential) 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 efficient optimal and near-optimal results, and also provide a brute-force integer linear programming approach for complete solutions to smaller instances.

Original languageEnglish
JournalNatural Computing
Volume17
Issue number4
Pages (from-to)693-707
ISSN1567-7818
DOIs
Publication statusPublished - 2018

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DNA
DNA sequences
Linear programming
Costs

Keywords

  • Cheminformatics
  • DNA-templated synthesis
  • Graphs
  • Optimization
  • Trees

Cite this

Hansen, Bjarke N. ; Larsen, Kim S. ; Merkle, Daniel ; Mihalchuk, Alexei. / DNA-templated synthesis optimization. In: Natural Computing. 2018 ; Vol. 17, No. 4. pp. 693-707.
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DNA-templated synthesis optimization. / Hansen, Bjarke N.; Larsen, Kim S.; Merkle, Daniel; Mihalchuk, Alexei.

In: Natural Computing, Vol. 17, No. 4, 2018, p. 693-707.

Research output: Contribution to journalJournal articleResearchpeer-review

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AU - Hansen, Bjarke N.

AU - Larsen, Kim S.

AU - Merkle, Daniel

AU - Mihalchuk, Alexei

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AB - 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 (sequential) 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 efficient optimal and near-optimal results, and also provide a brute-force integer linear programming approach for complete solutions to smaller instances.

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