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scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures

Authors David Doty , Benjamin L Lee , Tristan Stérin

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Author Details

David Doty
  • University of California, Davis, CA, USA
Benjamin L Lee
  • University of California, Davis, CA, USA
Tristan Stérin
  • Maynooth University, Ireland

Funding

  • Doty, David: Supported by NSF grants 1619343, 1900931, and CAREER grant 1844976.
  • Lee, Benjamin L: Supported by REU supplement through NSF CAREER grant 1844976.
  • Stérin, Tristan: Supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 772766, Active-DNA project), and Science Foundation Ireland (SFI) under Grant number 18/ERCS/5746.

Acknowledgements

We thank Matthew Patitz for beta-testing and feedback, and Pierre-Étienne Meunier, author of codenano, for valuable discussions regarding the data model/file format. We are grateful to anonymous reviewers whose detailed feedback has increased the presentation quality.

Cite AsGet BibTex

David Doty, Benjamin L Lee, and Tristan Stérin. scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
https://doi.org/10.4230/LIPIcs.DNA.2020.9

Abstract

We introduce scadnano (short for "scriptable cadnano"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano [Douglas et al., 2009], the most widely-used software for designing DNA origami [Paul W. K. Rothemund, 2006], with three main differences: 1) scadnano runs entirely in the browser, with no software installation required. 2) scadnano designs, while they can be edited manually, can also be created and edited by a well-documented Python scripting library, to help automate tedious tasks. 3) The scadnano file format is easily human-readable. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami.

Subject Classification

ACM Subject Classification
  • Applied computing → Computer-aided design
Keywords
  • computer-aided design
  • structural DNA nanotechnology
  • DNA origami

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Supplementary Materials

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