DNA-Templated Synthesis

This web-page is intended to illustrate algorithms for the optimization of DNA-Templated Synthesis Programs. As objectives we minimize the number of different tags or strands to be used under various conditions.

This page accompanies the paper

  • DNA-Templated Synthesis Optimization
    Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, Alexei Mihalchuk Natural Computing, 17(4): 693-707, 2018 [DOI]

Note that in the paper we are using renamed operations. Furthermore, we are using the 3’ and 5’ notation here (as commonly used in biology) for the tag positioning, and the orientation of strands used in the example programs below is adapted in an obvious (more biological) manner.

The traversal order is given based on the labels in the reaction nodes (squares). In the figures of the paper the intermediate compounds are not depicted to reduce clutter. The traversal order in case of subtrees of identical Strahler number is arbitrarily chosen here (in the paper: left first). The strand from the set of available strands is arbitrarily chosen here (in the paper, lexicographically smallest first).

DNA-Templated Programs

Please select an example and press “update”. Then the view of “Synthesis Plan”, “Program”, and “Statistics” are available. The synthesis plan allows for zooming. You can also edit the program or write your own and use update after your changes are done. In the “programs” view this will then show the sequence of states of your one-pot synthesis.

Note If the frame below is empty the playground server is temporarily offline.