Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks

  • Paul W. K. Rothemund
Part of the Natural Computing Series book series (NCS)


Planar Graph American Chemical Society Helical Domain Schlegel Diagram Polygonal Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    L.M. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266:1021–1024, 1994.Google Scholar
  2. 2.
    J. Chen and N.C. Seeman. The synthesis from DNA of a molecule with the connectivity of a cube. Nature, 350:631–633, 1991.CrossRefGoogle Scholar
  3. 3.
    D.R. Duckett, A.I.H. Murchie, S. Diekmann, E. von Kitzing, B. Kemper, and D.M.J. Lilley. The structure of the Holliday junction, and its resolution. Cell, 55:79–89, 1988.CrossRefGoogle Scholar
  4. 4.
    T.-J. Fu and N.C. Seeman. DNA double-crossover molecules. Biochemistry, 32:3211–3220, 1993.CrossRefGoogle Scholar
  5. 5.
    Y. He, Y. Chen, H. Liu, A.E. Ribbe, and C. Mao. Self-assembly of hexagonal DNA two-dimensional (2D) arrays. Journal of the American Chemical Society, 10:1021, 2005.Google Scholar
  6. 6.
    T.H. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, J.H. Reif, and N.C. Seeman. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. Journal of the American Chemical Society, 122:1848–1860, 2000.CrossRefGoogle Scholar
  7. 7.
    C. Mao, T.H. LaBean, J.H. Reif, and N.C. Seeman. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature, 407(6803):493–496, 2000.CrossRefGoogle Scholar
  8. 8.
    C.D. Mao, W.Q. Sun, and N.C. Seeman. Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy. Journal of the American Chemical Society, 121:5437–5443, 1999.CrossRefGoogle Scholar
  9. 9.
    A.I.H. Murchie, R.M. Clegg, E. von Kitzing, D.R. Duckett, S. Diekmann, and D.M.J. Lilley. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature, 341:763–766, 1989.CrossRefGoogle Scholar
  10. 10.
    P.W.K. Rothemund, N. Papadakis, and E. Winfree. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology, 2(12):e424, 2004.CrossRefGoogle Scholar
  11. 11.
    P.W.K. Rothemund. Generation of arbitrary nanoscale shapes and patterns by scaffolded DNA origami. (submitted), 2005.Google Scholar
  12. 12.
    P. W. K. Rothemund, A. Ekani-Nkodo, N. Papadakis, A. Kumar, D.K. Fygenson, E. Winfree. Design and characterization of programmable DNA nanotubes. Journal of the American Chemical Society, 26(50):16344–16353, 2004.CrossRefGoogle Scholar
  13. 13.
    P.W.K. Rothemund. DNA self-assembly with floppy motifs — single crossover lattices. Foundations of Nanoscience, Self-Assembled Architectures and Devices, Proceedings of FNANO’05 (J.H. Reif eds.) 185–186, 2005.Google Scholar
  14. 14.
    N.C. Seeman. Nucleic-acid junctions and lattices. Journal of Theoretical Biology, 99:237–247, 1982.CrossRefGoogle Scholar
  15. 15.
    N.C. Seeman. Construction of three-dimensional stick figures from branched DNA. DNA and Cell Biology, 7(10):475–486, 1991.CrossRefGoogle Scholar
  16. 16.
    Z.Y. Shen, H. Yan, T. Wang, and N.C. Seeman. Paranemic crossover DNA: A generalized Holliday structure with applications in nanotechnology. Journal of the American Chemical Society, 126:1666–1674, 2004.CrossRefGoogle Scholar
  17. 17.
    W.B. Sherman and N.C. Seeman. A precisely controlled DNA biped walking device. Nanoletters, 4(7):1203–1207, 2004.Google Scholar
  18. 18.
    W.B. Sherman and N.C. Seeman. The design of nucleic acid nanotubes. Journal of Biomolecular Structure and Dynamics, 20(6):930–931, 2003.Google Scholar
  19. 19.
    W.M. Shih, J.D. Quispe, and G.F. Joyce. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature, 427(6453):618–621, 2004.CrossRefGoogle Scholar
  20. 20.
    J.S. Shin and N.A. Pierce. A synthetic DNA walker for molecular transport. Journal of the American Chemical Society, 126(35):10834–10835, 2004.CrossRefGoogle Scholar
  21. 21.
    E. Winfree. On the computational power of DNA annealing and ligation. In R.J. Lipton and E.B. Baum, editors, DNA Based Computers, DIMACS, AMS Press, Providence, RI, 27:199–221, 1996.Google Scholar
  22. 22.
    E. Winfree, F. Liu, L.A. Wenzler, and N.C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539–544, 1998.CrossRefGoogle Scholar
  23. 23.
    H. Yan, X. Zhang, Z. Shen, and N.C. Seeman. A robust DNA mechanical device controlled by hybridization topology. Nature, 415:62–65, 2002.CrossRefGoogle Scholar
  24. 24.
    H. Yan, S.H. Park, G. Finkelstein, J.H. Reif, and T.H. LaBean. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 301:1882–1884, 2003.CrossRefGoogle Scholar
  25. 25.
    P. Yin, H. Yan, X.G. Daniell, A.J. Turberfield, and J.H. Reif. A unidirectional DNA walker that moves autonomously along a track. Angewandte Chemie International Edition, 43(37):4906–4911, 2004.CrossRefGoogle Scholar
  26. 26.
    B. Yurke, A.J. Turberfield, A.P. Mills, Jr., F.C. Simmel, and J.L. Neumann. A DNA-fuelled molecular machine made of DNA. Nature, 406:605–608, 2000.CrossRefGoogle Scholar
  27. 27.
    Y. Zhang and N.C. Seeman. The construction of a DNA truncated octahedron. Journal of the American Chemical Society, 116:1661–1669, 1994.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Paul W. K. Rothemund
    • 1
  1. 1.California Institute of TechnologyPasadenaUSA

Personalised recommendations