Skip to main content

Structural DNA Nanotechnology: Molecular Construction and Computation

  • Conference paper
Book cover Unconventional Computation (UC 2005)

Abstract

Structural DNA nanotechnology entails the construction of objects, lattices and devices from branched DNA molecules. Branched DNA molecules open the way for the construction of a variety of N-connected motifs. These motifs can be joined by cohesive interactions to produce larger constructs in a bottom-up approach to nanoconstruction. The first objects produced by this approach were stick polyhedra and topological targets, such as knots and Borromean rings. These were followed by periodic arrays with programmable patterns. It is possible to exploit DNA structural transitions and sequence-specific binding to produce a variety of DNA nanomechanical devices, which include a bipedal walker and a machine that emulates the translational capabilities of the ribosome. Much of the promise of this methodology involves the use of DNA to scaffold other materials, such as biological macromolecules, nanoelectronic components, and polymers. These systems are designed to lead to improvements in crystallography, computation and the production of diverse and exotic materials. Branched DNA can be used to emulate Wang tiles, and it can be used to construct arbitrary irregular graphs and to address their colorability.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Cohen, S.N., Chang, A.C.Y., Boyer, H.W., Helling, R.B.: Construction of Biologically Functional Bacterial Plasmids in vitro. Proc. Nat. Acad. Sci (USA) 70, 3240–3244 (1973)

    Article  Google Scholar 

  2. Qiu, H., Dewan, J.C., Seeman, N.C.: A DNA Decamer with a Sticky End: The Crystal Structure of d-CGACGATCGT. J. Mol. Biol. 267, 881–898 (1997)

    Article  Google Scholar 

  3. Seeman, N.C.: DNA Nicks and Nodes and Nanotechnology. NanoLetts. 1, 22–26 (2001)

    Google Scholar 

  4. Seeman, N.C.: Nucleic Acid Junctions and Lattices. J. Theor. Biol. 99, 237–247 (1982)

    Article  Google Scholar 

  5. Chen, J., Seeman, N.C.: The Synthesis from DNA of a Molecule with the Connectivity of a Cube. Nature 350, 631–633 (1991)

    Article  Google Scholar 

  6. Zhang, Y., Seeman, N.C.: The Construction of a DNA Truncated Octahedron. J. Am. Chem. Soc. 116, 1661–1669 (1994)

    Article  Google Scholar 

  7. Wang, Y., Mueller, J.E., Kemper, B., Seeman, N.C.: The Assembly and Characterization of 5-Arm and 6-Arm DNA Junctions. Biochem. 30, 5667–5674 (1991)

    Article  Google Scholar 

  8. Seeman, N.C.: The Design of Single-Stranded Nucleic Acid Knots. Molec. Eng. 2, 297–307 (1992)

    Article  Google Scholar 

  9. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and Self-Assembly of Two-Dimensional DNA Crystals. Nature 394, 539–544 (1998)

    Article  Google Scholar 

  10. Liu, F., Sha, R., Seeman, N.C.: Modifying the Surface Features of Two-Dimensional DNA Crystals. J. Am. Chem. Soc. 121, 917–922 (1999)

    Article  Google Scholar 

  11. Mao, C., Sun, W., Seeman, N.C.: Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999)

    Article  Google Scholar 

  12. Ding, B., Sha, R., Seeman, N.C.: Pseudohexagonal 2D DNA Crystals from Double Crossover Cohesion. J. Am. Chem. Soc. 126, 10230–10231 (2004)

    Article  Google Scholar 

  13. Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  14. Winfree, E.: In DNA Based Computers. In: Lipton, R.J., Baum, E.B. (eds.) Proceedings of a DIMACS Workshop, Princeton University, Am. Math. Soc., Providence, On the computational power of DNA annealing and ligation, April 4, 1995, pp. 199–219 (1996)

    Google Scholar 

  15. Mao, C., LaBean, T., Reif, J.H., Seeman, N.C.: Logical Computation Using Algorithmic Self-Assembly of DNA Triple Crossover Molecules. Nature 407, 493–496 (2000)

    Article  Google Scholar 

  16. Jonoska, N., Karl, S.A., Saito, M.: 3D DNA Structures in Computing. Biosystems 52, 143–153 (1999)

    Article  Google Scholar 

  17. Sa-Ardyen, P., Jonoska, N., Seeman, N.C.: The Construction of Graphs Whose Edges are DNA Helix Axes. J. Am. Chem. Soc. 126, 6648–6657 (2004)

    Article  Google Scholar 

  18. Mao, C., Sun, W., Shen, Z., Seeman, N.C.: A DNA Nanomechanical Device Based on the B-Z Transition. Nature 397, 144–146 (1999)

    Article  Google Scholar 

  19. Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A Robust DNA Mechanical Device Controlled by Hybridization Topology. Nature 415, 62–65 (2002)

    Article  Google Scholar 

  20. Yurke, B., Turberfield, A.J., Mills Jr., A.P., Simmel, F.C., Newmann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)

    Article  Google Scholar 

  21. Liao, S., Seeman, N.C.: Translation of DNA Signals into Polymer Assembly Instructions. Science 306, 2072–2074 (2004)

    Article  Google Scholar 

  22. Sherman, W.B., Seeman, N.C.: A Precisely Controlled DNA Bipedal Walking Device. NanoLetts. 4, 1203–1207 (2004)

    Google Scholar 

  23. Robinson, B.H., Seeman, N.C.: The Design of a Biochip: A Self-Assembling Molecular-Scale Memory Device. Protein Eng. 1, 295–300 (1987)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Sha, R. et al. (2005). Structural DNA Nanotechnology: Molecular Construction and Computation. In: Calude, C.S., Dinneen, M.J., Păun, G., Pérez-Jímenez, M.J., Rozenberg, G. (eds) Unconventional Computation. UC 2005. Lecture Notes in Computer Science, vol 3699. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560319_4

Download citation

  • DOI: https://doi.org/10.1007/11560319_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29100-8

  • Online ISBN: 978-3-540-32022-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics