Document Open Access Logo

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

Authors David Doty , Benjamin L Lee , Tristan Stérin

PDF
Thumbnail PDF

File

LIPIcs.DNA.2020.9.pdf
  • Filesize: 1.87 MB
  • 17 pages

Document Identifiers

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 As Get 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

Metrics

  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    0
    PDF Downloads
    0
    Metadata Views

Supplementary Materials

References

  1. Brython. URL: https://brython.info/.
  2. cadnano v2.5. URL: https://github.com/cadnano/cadnano2.5.
  3. cadnano v2.5 Python API. URL: https://cadnano.readthedocs.io/en/master/scripting.html.
  4. Cando. URL: https://cando-dna-origami.org/.
  5. codenano. URL: https://dna.hamilton.ie/2019-07-18-codenano.html.
  6. Dart programming language. URL: https://dart.dev/.
  7. Elm programming language. URL: https://elm-lang.org/.
  8. IDT DNA modifications. URL: https://www.idtdna.com/pages/products/custom-dna-rna/oligo-modifications.
  9. Json (javascript object notation). URL: https://www.json.org/json-en.html.
  10. Overreact Dart library. URL: https://pub.dev/packages/over_react.
  11. Pyodide. URL: https://github.com/iodide-project/pyodide.
  12. React Javascript library. URL: https://reactjs.org/.
  13. Redux Dart library. URL: https://pub.dev/packages/redux.
  14. Redux Javascript library. URL: https://redux.js.org/.
  15. Skulpt. URL: https://skulpt.org/.
  16. Unidirectional data flow in Redux. URL: https://redux.js.org/basics/data-flow.
  17. SAMSON, the open molecular modeling platform. https://www.samson-connect.net, 2019.
  18. Erik Benson, Abdulmelik Mohammed, Johan Gardell, Sergej Masich, Eugen Czeizler, Pekka Orponen, and Björn Högberg. DNA rendering of polyhedral meshes at the nanoscale. Nature, 523(7561):441-444, July 2015. URL: https://doi.org/10.1038/nature14586.
  19. Erik Benson, Abdulmelik Mohammed, Johan Gardell, Sergej Masich, Eugen Czeizler, Pekka Orponen, and Björn Högberg. DNA rendering of polyhedral meshes at the nanoscale. Nature, 523(7561):441-444, 2015. Google Scholar
  20. Gourab Chatterjee, Neil Dalchau, Richard A Muscat, Andrew Phillips, and Georg Seelig. A spatially localized architecture for fast and modular DNA computing. Nature nanotechnology, 12(9):920, 2017. Google Scholar
  21. Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J. Wilson, Morgan Beeby, Ivan Viola, and Ivan Barisic. Adenita: Interactive 3D modeling and visualization of DNA nanostructures. Technical report, bioRxiv, 2019. URL: https://doi.org/10.1101/849976.
  22. Hendrik Dietz, Shawn M Douglas, and William M Shih. Folding DNA into twisted and curved nanoscale shapes. Science, 325(5941):725-730, 2009. Google Scholar
  23. Shawn M Douglas, Hendrik Dietz, Tim Liedl, Björn Högberg, Franziska Graf, and William M Shih. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245):414-418, 2009. Google Scholar
  24. Shawn M Douglas, Adam H Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M Church, and William M Shih. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15):5001-5006, 2009. URL: https://cadnano.org/.
  25. Erich Gamma, Richard Helm, Ralph Johnson, and John Vlissides. Design patterns: Elements of reusable object-oriented software. Pearson Education India, 1995. Google Scholar
  26. Hongzhou Gu, Jie Chao, Shou-Jun Xiao, and Nadrian C Seeman. A proximity-based programmable DNA nanoscale assembly line. Nature, 465(7295):202-205, 2010. Google Scholar
  27. Dongran Han, Suchetan Pal, Jeanette Nangreave, Zhengtao Deng, Yan Liu, and Hao Yan. DNA origami with complex curvatures in three-dimensional space. Science, 332(6027):342-346, 2011. Google Scholar
  28. Hyungmin Jun, Xiao Wang, William Bricker, Steve Jackson, and Mark Bathe. Rapid prototyping of wireframe scaffolded DNA origami using ATHENA. Technical report, bioRxiv, 2020. URL: https://doi.org/10.1101/2020.02.09.940320.
  29. Glenn Krasner and Stephen Pope. A cookbook for using the model-view-controller user interface paradigm in Smalltalk-80. Journal of object-oriented programming, 1, 1988. Google Scholar
  30. Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, and Ivo L Hofacker. ViennaRNA package 2.0. Algorithms for Molecular Biology, 6(1), November 2011. URL: https://doi.org/10.1186/1748-7188-6-26.
  31. Christopher Maffeo and Aleksei Aksimentiev. MrDNA: A multi-resolution model for predicting the structure and dynamics of nanoscale dna objects. bioRxiv, 2019. URL: https://doi.org/10.1101/865733.
  32. Dionis Minev, Christopher M. Wintersinger, Anastasia Ershova, and William M Shih. Robust nucleation control via crisscross polymerization of DNA slats. Technical report, biorXiv, 2019. URL: https://www.biorxiv.org/content/10.1101/2019.12.11.873349v1.
  33. Paul W. K. Rothemund. Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082):297-302, 2006. Google Scholar
  34. Marc Shapiro, Nuno Preguiça, Carlos Baquero, and Marek Zawirski. Conflict-free replicated data types. In SSS 2011: Symposium on self-stabilizing systems, pages 386-400, 2011. Google Scholar
  35. Benedict EK Snodin, Ferdinando Randisi, Majid Mosayebi, Petr Šulc, John S Schreck, Flavio Romano, Thomas E Ouldridge, Roman Tsukanov, Eyal Nir, Ard A Louis, and Jonathan P. K. Doye. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. The Journal of chemical physics, 142(23):234901, 2015. Google Scholar
  36. Anupama J Thubagere, Wei Li, Robert F Johnson, Zibo Chen, Shayan Doroudi, Yae Lim Lee, Gregory Izatt, Sarah Wittman, Niranjan Srinivas, Damien Woods, Erik Winfree, and Lulu Qian. A cargo-sorting DNA robot. Science, 357(6356):eaan6558, 2017. Google Scholar
  37. Grigory Tikhomirov, Philip Petersen, and Lulu Qian. Programmable disorder in random DNA tilings. Nature nanotechnology, 12(3):251, 2017. Google Scholar
  38. Petr Šulc, Flavio Romano, Thomas E. Ouldridge, Lorenzo Rovigatti, Jonathan P. K. Doye, and Ard A. Louis. Sequence-dependent thermodynamics of a coarse-grained DNA model. The Journal of Chemical Physics, 137(13):135101, 2012. URL: https://doi.org/10.1063/1.4754132.
  39. Bryan Wei, Mingjie Dai, and Peng Yin. Complex shapes self-assembled from single-stranded DNA tiles. Nature, 485(7400):623-626, 2012. Google Scholar
  40. Erik Winfree, Furong Liu, Lisa A Wenzler, and Nadrian C Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394(6693):539-544, 1998. Google Scholar
  41. Sungwook Woo and Paul WK Rothemund. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry, 3(8):620, 2011. Google Scholar
  42. Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, and Erik Winfree. Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature, 567:366-372, 2019. URL: https://doi.org/10.1038/s41586-019-1014-9.
  43. Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, and Niles A. Pierce. Nupack: Analysis and design of nucleic acid systems. Journal of Computational Chemistry, 32(1):170-173, 2011. URL: https://doi.org/10.1002/jcc.21596.
  44. Fei Zhang, Shuoxing Jiang, Siyu Wu, Yulin Li, Chengde Mao, Yan Liu, and Hao Yan. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nature nanotechnology, 10(9):779, 2015. Google Scholar
Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact