Nicks, Nodes, and New Motifs for DNA Nanotechnology

  • Nadrian C. Seeman
  • Chengde Mao
  • Furong Liu
  • Ruojie Sha
  • Xiaoping Yang
  • Lisa Wenzler
  • Xiaojun Li
  • Zhiyong Shen
  • Hao Yan
  • Phiset Sa-Ardyen
  • Xiaoping Zhang
  • Wanqiu Shen
  • Jeff Birac
  • Philip Lukeman
  • Yariv Pinto
  • Xiaojun Li
  • Jing Qi
  • Bing Liu
  • Hangxia Qiu
  • Shouming Du
  • Hui Wang
  • Weiqiong Sun
  • Yinli Wang
  • Tsu-Ju Fu
  • Yuwen Zhang
  • John E. Mueller
  • Junghuei Chen
Chapter
Part of the NATO Science Series book series (NAII, volume 6)

Abstract

The properties that make DNA such an effective molecule for its biological role as genetic material also make it a superb molecule for nanoconstruction. One key to using DNA for this purpose is to produce stable complex motifs, such as branched molecules. Combining branched species by sticky ended interactions, leads to N- connected stick figures whose edges consist of double helical DNA. Zero node removal or reciprocal crossover, leads to complex fused motifs, such as rigid multi-crossover molecules and paranemic crossover molecules. Multi-crossover molecules have been used to produce 2D arrays and a nanomechanical device. Algorithmic assembly and the use of complex complementarities for joining units are goals in progress that are likely to produce new capabilities for DNA nanotechnology.

Keywords

Sugar Crystallization Hydroxyl Cage Recombination 

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References

  1. 1.
    Watson, J.D.; Crick, F.H. (1953), Nature (London) 171, 737–738.ADSCrossRefGoogle Scholar
  2. 2.
    Cohen, S.N.; Chang, A.C.Y.; Boyer, H.W.; Helling, R.B. (1973), Proc. Nat. Acad. Sci. (USA) 70, 3240–3244.ADSCrossRefGoogle Scholar
  3. 3.
    Seeman, N.C. (1982), J. Theor. Biol. 99, 237–247.CrossRefGoogle Scholar
  4. 4.
    Seeman, N.C. (1999), Trends Biotech. 17, 437–443.CrossRefGoogle Scholar
  5. 5.
    Adleman L. (1994), Science 266, 1021–1024.ADSCrossRefGoogle Scholar
  6. 6.
    Seeman, N.C. (2000), Synlett, in press.Google Scholar
  7. 7.
    Voet, D.; Rich, A. (1970), Prog. Nucl. Acid Res. Mol. Biol. 10, 183–265.CrossRefGoogle Scholar
  8. 8.
    Fahlman, R.P.; Sen, D. (1999), J. Am. Chem.Soc. 121, 11079–11085.CrossRefGoogle Scholar
  9. 9.
    Protozanova E.; Macgregor R.B. Jr. (1996), Biochem. 35, 16638–16645.CrossRefGoogle Scholar
  10. 10.
    Qiu, H; Dewan, J.C.; Seeman, N.C. (1997), J. Mol. Biol. 267, 881–898.CrossRefGoogle Scholar
  11. 11.
    Seeman, N.C; Chen, J.; Du, S.M.; Mueller, IE.; Zhang, Y.; Fu, T.-J.; Wang, H.; Wang, Y.; Zhang, S. (1993), New J. Chem. 17, 739–755.Google Scholar
  12. 12.
    White, J.H.; Millett, K.C.; Cozzarelli, N.R. (1987), J Mol. Biol 197, 585–603.CrossRefGoogle Scholar
  13. 13.
    Fu, T.-J.; Seeman, N.C. (1993), Biochem. 32, 3211–3220.CrossRefGoogle Scholar
  14. 14.
    Liu, B.; Leontis, N.B.; N.C. Seeman (1994), Nanobiol. 3, 177–188.Google Scholar
  15. 15.
    Holliday, R. (1964), Genet Res. 5, 282–304.CrossRefGoogle Scholar
  16. 16.
    Ma, R.-I.; Kallenbach, N.R.; Sheardy, R.D.; Petrillo, M.L.; Seeman, N.C. (1986), Nucl. Acids Res. 14, 9745–9753.CrossRefGoogle Scholar
  17. 17.
    Kallenbach, N.R.; Ma, R.-I.; Seeman, N.C. (1983), Nature (London) 305, 829–831.ADSCrossRefGoogle Scholar
  18. 18.
    Wang, Y.; Mueller, J.E.; Kemper, B.; Seeman, N.C. (1991), Biochem. 30, 5667–5674.CrossRefGoogle Scholar
  19. 19.
    Mao, C.; Sun, W.; Seeman, N.C. (1999), J. Am. Chem.Soc. 121, 5437–5443.CrossRefGoogle Scholar
  20. 20.
    Petrillo, M.L.; Newton, C.J.; Cunningham, R.P.; R.-I. Ma; Kallenbach, N.R.; Seeman, N.C. (1988), Biopolymers 27, 1337–1352.CrossRefGoogle Scholar
  21. 21.
    Wells, A. F. (1977), Three-dimensional Nets and Polyhedra, John Wiley & Sons, New York.Google Scholar
  22. 22.
    Williams, R. (1979), The Geometrical Foundation of Natural Structure, Dover, New York.Google Scholar
  23. 23.
    Robinson, B.H.; Seeman, N.C. (1987), Prot. Eng. 1, 295–300.CrossRefGoogle Scholar
  24. 24.
    Winfree, E. (1995), In: DNA Based Computers, ed. by R. Lipton and E. Baum, Am. Math. Soc, Providence, pp. 199–215.Google Scholar
  25. 25.
    Chen, J.; Seeman, N. C. (1991), Nature (London) 350, 631–633.ADSCrossRefGoogle Scholar
  26. 26.
    Zhang, Y.; Seeman, N.C. (1992), J. Am. Chem. Soc. 114, 2656–2663.CrossRefGoogle Scholar
  27. 27.
    Zhang, Y.; Seeman, N.C. (1994), J. Am. Chem.Soc. 116, 1661–1669.CrossRefGoogle Scholar
  28. 28.
    Thaler, D.S.; Stahl, F.W. (1988), Ann. Rev. Genet. 22, 169–197.CrossRefGoogle Scholar
  29. 29.
    Sun, H.; Treco, D.; Szostak, J.W. (1991), Cell 64, 1155–1161.CrossRefGoogle Scholar
  30. 30.
    Schwacha, A.; Kleckner. N. (1995), Cell 83,783–791.CrossRefGoogle Scholar
  31. 31.
    Li, X.; Yang, X.; Qi, J.; Seeman, N.C. (1996), J. Am. Chem. Soc. 118, 6131–6140.CrossRefGoogle Scholar
  32. 32.
    Winfree, E.; Liu, F.; Wenzler, L.A.; Seeman, N.C. (1998), Nature 394, 539–544.ADSCrossRefGoogle Scholar
  33. 33.
    Liu, F.; Sha, R.; Seeman, N.C. (1999), J. Am. Chem. Soc. 121, 917–922.CrossRefGoogle Scholar
  34. 34.
    LaBean, T.; Yan, H,;. Kopatsch, J.; Liu, F.; Winfree, E.; Reif, J.H.; Seeman, N.C. (2000), J. Am. Chem.Soc. 122, 1848–1860.CrossRefGoogle Scholar
  35. 35.
    Mao, C.; Sun, W.; Shen, Z.; Seeman, N.C. (1999), Nature (London) 397, 144–146.ADSCrossRefGoogle Scholar
  36. 36.
    Rich, A.; Nordheim, A.; Wang, A.H.-J. (1984), Ann. Rev. Biochem. 53, 791–846.CrossRefGoogle Scholar
  37. 37.
    Behe, M.; Felsenfeld, G. (1981), Proc. Nat. Acad. Sci. (USA) 78, 1619–1623.ADSCrossRefGoogle Scholar
  38. 38.
    Churchill, M.E.A.; Tullius, T.D.; Kallenbach, N.R.; Seeman, N.C. (1988), Proc. Nat.Acad.Sci. USA 85, 4653–4656.ADSCrossRefGoogle Scholar
  39. 39.
    Murchie, A.I.H.; Clegg, R.M.; von Kitzing, E.; Duckett, D.R.; Diekmann, S.; Lilley, D.M.J, (1989), Nature (London) 341, 763–766.ADSCrossRefGoogle Scholar
  40. 40.
    Fu, T.J.; Tse-Dinh, Y.C.; Seeman N.C. (1994), J. Mol. Biol. 236, 91–105.CrossRefGoogle Scholar
  41. 41.
    Shen, Z. (1999), Ph.D. Thesis, New York University.Google Scholar
  42. 42.
    Liu, F.; Wang, H.; Seeman, N.C. (1999), Nanobiol. 4, 257–262.Google Scholar
  43. 43.
    Zhang, K.; Taylor, J.-S., (1999) J. Am. Chem. Soc. 121, 11579–11580.CrossRefGoogle Scholar
  44. 44.
    Yang, X.; Wenzler, L.A.; Qi, J.; Li, X.; Seeman, N.C. (1998), J. Am. Chem. Soc. 120, 9779–9786.CrossRefGoogle Scholar
  45. 45.
    Schrödinger, E. (1967), What is Life? and Mind and Matter, Cambridge Univ. Press, Cambridge, pp. 60–71.Google Scholar
  46. 46.
    Wang, H. (1963), In Proc. Symp. Math. Theory of Automata, Polytechnic Press, New York, pp. 23–26.Google Scholar
  47. 47.
    Grünbaum, B.; Shephard, G.C. (1987), Tilings & Patterns, W.H. Freeman & Co., New York, pp. 583–608.MATHGoogle Scholar
  48. 48.
    Colbert, D.T.; Zhang, J.; McClure, S.M.; Nikolaev, P.; Chen, Z.; Hafner, J.H.; Owens, D.W.; Kotula, P.G.; Carter, C.B.; Weaver, J.H.; Rinzler A.G.; Smalley, R.E. (1994), Science 266, 1218–1222.ADSCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2000

Authors and Affiliations

  • Nadrian C. Seeman
    • 1
  • Chengde Mao
    • 1
  • Furong Liu
    • 1
  • Ruojie Sha
    • 1
  • Xiaoping Yang
    • 1
  • Lisa Wenzler
    • 1
  • Xiaojun Li
    • 1
  • Zhiyong Shen
    • 1
  • Hao Yan
    • 1
  • Phiset Sa-Ardyen
    • 1
  • Xiaoping Zhang
    • 1
  • Wanqiu Shen
    • 1
  • Jeff Birac
    • 1
  • Philip Lukeman
    • 1
  • Yariv Pinto
    • 1
  • Xiaojun Li
    • 1
  • Jing Qi
    • 1
  • Bing Liu
    • 1
  • Hangxia Qiu
    • 1
  • Shouming Du
    • 1
  • Hui Wang
    • 1
  • Weiqiong Sun
    • 1
  • Yinli Wang
    • 1
  • Tsu-Ju Fu
    • 1
  • Yuwen Zhang
    • 1
  • John E. Mueller
    • 1
  • Junghuei Chen
    • 1
  1. 1.Department of ChemistryNew York UniversityNew YorkUSA

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