DnaOS

Cite

How to cite DnaOS

If DnaOS helped a figure, a thesis chapter, or a class report, please cite the studio so others can find it.

Please mention the tool in your article — or in whatever you used it for: a paper, thesis, poster, talk, or class report.

If you publish work that used DnaOS, please keep this citation request visible so the studio stays findable.

This is a courtesy citation, not a claim of authorship over your DNA designs. Your sequences and figures remain yours. DnaOS is licensed under GPL-3.0 — see License.

Methods papers

Scientific methods used in DnaOS (origami, honeycomb lattices, cages, DX tiles, nearest-neighbor thermodynamics, coarse-grained MD, and spanning-tree routing). Same list as Foundations on the home page. Cite a paper in addition to DnaOS when that method is relevant — not as a claim that DnaOS is affiliated with those groups.

  1. 1.
    Scaffolded origami

    Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006). https://doi.org/10.1038/nature04586

  2. 2.
    3D honeycomb origami

    Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F. & Shih, W. M. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009). https://doi.org/10.1038/nature08016

  3. 3.
    Twist and curve

    Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009). https://doi.org/10.1126/science.1174251

  4. 4.
    Top-down 3D cages

    Veneziano, R. et al. Designer nanoscale DNA assemblies programmed from the top down. Science 352, aaf4388 (2016). https://doi.org/10.1126/science.aaf4388

  5. 5.
    Free-form 2D origami

    Jun, H. et al. Autonomously designed free-form 2D DNA origami. Sci. Adv. 5, eaav0655 (2019). https://doi.org/10.1126/sciadv.aav0655

  6. 6.
    DX molecules

    Fu, T. J. & Seeman, N. C. DNA double-crossover molecules. Biochemistry 32, 3211–3220 (1993). https://doi.org/10.1021/bi00064a003

  7. 7.
    Antiparallel DX tiles

    Li, X., Yang, X., Qi, J. & Seeman, N. C. Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Am. Chem. Soc. 118, 6131–6140 (1996). https://doi.org/10.1021/ja960307r

  8. 8.
    2D DX crystals

    Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998). https://doi.org/10.1038/28998

  9. 9.
    DAE ligation periodicity

    Sa-Ardyen, P., Vologodskii, A. V. & Seeman, N. C. The flexibility of DNA double crossover molecules. Biophys. J. 84, 3829–3837 (2003). https://doi.org/10.1016/S0006-3495(03)75110-8

  10. 10.
    Nearest-neighbor Tm

    SantaLucia, J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 95, 1460–1465 (1998). https://doi.org/10.1073/pnas.95.4.1460

  11. 11.
    oxDNA model

    Ouldridge, T. E., Louis, A. A. & Doye, J. P. K. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J. Chem. Phys. 134, 085101 (2011). https://doi.org/10.1063/1.3552946

  12. 12.
    Prim tree

    Prim, R. C. Shortest connection networks and some generalizations. Bell Syst. Tech. J. 36, 1389–1401 (1957). https://doi.org/10.1002/j.1538-7305.1957.tb01515.x