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James Parkin edited this page Dec 15, 2017 · 2 revisions

Designing DNA sequences with Piperine

Example workflow: Designing sequences for the rock-paper-scissors oscillator.

To start the design process, write a text file describing the CRN of interest, an oscillator. The rock-paper-scissors oscillator is a CRN of three species and three reactions. Make a file named rps.crn with the following contents:

B + A -> 2B
C + B -> 2C
A + C -> 2A

Use the piperine-design command-line utility to design sequences :

piperine-design rps.crn

Once Piperine is finished generating and scoring the design candidates, it will print the winning sequence index to the screen. At the end of this execution, 10 new files should exist: four *.seqs files, four *_strands.txt, the heuristics table, and the score report.

The *_strands.txt files contain sequence definitions of the strands designed by Piperine. For more information on interpreting the names given to sequences and complexes, look to reference [1].

Example workflow: Adjusting toehold parameters.

To start the design process, write a text file describing the CRN of interest, in this case a chaotic attractor. Make a file named RW.crn with the following contents:

a -> 2a
2a -> a
b + a -> 2b
b ->
a+c->
c->2c
c+c->c

Use the piperine-design command-line utility to design sequences :

piperine-design RW.crn

Piperine will not be able to produce sequences for this large of a reaction under the Srinivas2017 scheme and default toehold parameters. The error message will look similar to this:

RuntimeError: Cannot make toeholds to user specification! Try target energy:7.5, maxspurious:0.65, deviation:0.47, which makes 17 toeholds.

In the help message for this commandline utility (piperine-design -h) we can find the relevant options and adjust the toehold parameters accordingly.

piperine-design RW.crn -m 0.7 -d 0.5

Relieving the toehold energetics constraints allows Piperine to produce sequences for this CRN.

References

  1. Chen, Y. J. et al. Programmable chemical controllers made from DNA. Nat. Nanotechnol. 8, 755–762 (2013).
  2. Srinivas, N., Parkin, J., Seelig, G., Winfree, E. & Soloveichik, D. Enzyme-free nucleic acid dynamical systems. Science (80-. ). 358, (2017).

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