Hostname: page-component-745bb68f8f-5r2nc Total loading time: 0 Render date: 2025-01-14T02:25:53.741Z Has data issue: false hasContentIssue false
  • English
  • Français

The Control of Dna Structure and Topology: An Overview

Published online by Cambridge University Press:  15 February 2011

Nadrian C. Seeman ,
Yuwen Zhang ,
Shou Ming Du ,
Hui Wang ,
John E. Mueller ,
Yinli Wang ,
Bing Liu ,
Jing Qi  and
Junghuei Chen
Nadrian C. Seeman
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Yuwen Zhang
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Shou Ming Du
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Hui Wang
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
John E. Mueller
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Yinli Wang
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Bing Liu
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Jing Qi
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Junghuei Chen
Affiliation:
Department of Chemistry, New York University, New York, NY 10003, USA
Get access

Abstract

The control of structure on the nanoscale relies on intermolecular interactions whose specificity and geometry can be treated on a predictive basis. DNA fulfills this criterion, and provides an extremely convenient construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of double helical DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct in solution a covalently closed DNA molecule whose helix axes have the connectivity of a cube: The molecule has twelve double helical edges; every edge is two helical turns in length, resulting in a hexacatenane, each of whose strands corresponds to a face of the object. We have developed a solid-support-based synthetic methodology that is more effective than solution synthesis. The key features of the technique are control over the formation of each edge of the object, and the topological closure of each intermediate. The isolation of individual objects on the surface of the support eliminates cross-reactions between growing products. The solid-support-based methodology has been used to construct a molecule whose helix axes have the connectivity of a truncated octahedron. This figure has 14 faces, of which six are square and eight are hexagonal; this Archimedean polyhedron contains 24 vertices and 36 edges, and is built from a 14-catenane of DNA. Knotted molecules appear to be the route for cloning DNA objects. It is possible to construct three knotted topologies, as well as a simple cyclic molecule from a single precursor, by control of solution conditions. Control of both branching and braiding topology is strong in this system, but control of 3-D structure remains elusive. Our key aim is the formation of prespecified 2-D and 3-D periodic structures for use in diffraction experiments. Another application envisioned is scaffolding for the assembly of molecular electronic devices.

Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 351: Symposium V – Molecularly Designed Ultrafine/Nanostructured Materials , 1994 , 57
Copyright
Copyright © Materials Research Society 1994

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

1. Drexler, K.E., Proc. Nad. Acad. Sci. (USA) 78, 5275–5278 (1981).Google Scholar
2. Seeman, N.C., Nanotechnol. 2, 149–159 (1991).Google Scholar
3. Medawar, P.B., The Art of the Soluble, (Methuen & Co., London 1967), p. 48.Google Scholar
4. Eigler, D.M. and Schweizer, E.K., Nature (London) 344, 524–526 (1990).Google Scholar
5. Eigler, D.M., Lutz, C.P. and Rudge, W.E., Nature (London) 352, 600–603 (1991).Google Scholar
6. Cohen, S.N., Chang, A.C.Y., Boyer, H.W. and Helling, R.B., Proc. Natl. Acad. Sci. (USA) 70, 3240–3244 (1973).Google Scholar
7. Seeman, N.C., J. Theor. Biol. 99, 237–247 (1982).Google Scholar
8. Seeman, N. C., J. Biomol. Str. & Dyns. 8, 573–581 (1990).Google Scholar
9. Kallenbach, N.R., Ma, R.-I. and Seeman, N.C., Nature, 305,829–831 (1983).Google Scholar
10. Wells, A.F., 3-D Nets and Polyhedra (John Wiley & Sons, New York, 1977).Google Scholar
11. Ma, R.-I., Kallenbach, N.R., Sheardy, R.D., Petrillo, M.L. and Seeman, N.C., Nucl. Acids Res. 14, 9745–9753 (1986).Google Scholar
12. Wang, Y., Mueller, J.E., Kemper, B., Seeman, N.C.,Biochem. 30, 5667–5674 (1991).Google Scholar
13. Petrillo, M.L., Newton, C.J., Cunningham, R.P., Ma, R.-I., Kallenbach, N.R. and Seeman, N.C., Biopolymers 27, 1337–1352 (1988).Google Scholar
14. Hagerman, P.J., Ann. Rev. Biophys. & Biophys. Chem. 17, 265–286 (1988).Google Scholar
15. Hustedt, E.J., Spaltenstein, A., Kirchner, J.J., Hopkins, P.B. and Robinson, B.H., Biochem. 32, 1774–1787 (1993).Google Scholar
16. Chen, J.-H., Kallenbach, N.R. and Seeman, N.C., J. Am. Chem. Soc. 111, 6402–6407 (1989).Google Scholar
17. Chen, J. and Seeman, N.C., Nature (London) 350, 631–633 (1991).Google Scholar
18. Chen, J. and Seeman, N.C., Electrophoresis 12, 607–611 (1991).Google Scholar
19. Zhang, Y. and Seeman, N.C., J. Am. Chem.Soc. 114, 2656–2663 (1992).Google Scholar
20. Zhang, Y. and Seeman, N.C., J. Am. Chem.Soc. 116, 1661–1669 (1994).Google Scholar
21. White, J.H., Millett, K.C., and Cozzarelli, N.R., J. Mol. Biol. 197, 585–603 (1987).Google Scholar
22. Seeman, N.C., DNA and Cell Biology 10, 475–486 (1991).Google Scholar
23. Mueller, J.E., Du, S.M. and Seeman, N.C., J.Am.Chem.Soc. 113,6306–6308 (1991).Google Scholar
24. Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G. and Rich, A., Nature (London) 282, 680–686 (1979).Google Scholar
25. Behe, M. and Felsenfeld, G., Proc. Natl. Acad. Sci. (USA) 78, 1619–1623 (1981).Google Scholar
26. Du, S.M., Stollar, B.D., and Seeman, N.C. (1994) (unpublished).Google Scholar
27. Du, S.M., Tse-Dinh, Y.-C., and Seeman, N.C. (1994) (unpublished).Google Scholar
28. Wang, H., Du, S.M. and Seeman, N.C., J. Biomol. Str.& Dyns. 10, 853–863 (1993).Google Scholar
29. Seeman, N.C., Molecular Engineering 2, 297–307 (1992).Google Scholar
30. Seeman, N.C., Chen, J., Du, S.M., Mueller, J.E., Zhang, Y., Fu, T.-J., Wang, H., Wang, Y., and Zhang, S., Synthetic DNA Knots and Catenanes, New J.Chem. 17, 739–755 (1993).Google Scholar
31. Du, S.M. and Seeman, N.C., Biopolymers 34, 31–37 (1994).Google Scholar
32. Caruthers, M. H., Science 230, 281–285 (1985).Google Scholar
33. Eckstein, F., Oligonucleotides and Analogues (IRL, Oxford, 1993), pp. 49–313.Google Scholar
34. Robinson, B.H. and Seeman, N.C., Prot. Eng. 1, 295–300 (1987).Google Scholar
35. Leontis, N.B., Hills, M.T., Piotto, M., Malhotra, A., Nussbaum, J. & Gorenstein, D.G. (1993), J. Biomol. Str. & Dyns. 11, 215–223.Google Scholar
36. Karrasch, S., Hegerl, R., Hoh, J.H., Baumeister, W., and Engle, A., Proc. Natl. Acad. Sci. (USA), 91, 836–838 (1994).Google Scholar
37. Bilderback, D.H., Hoffman, S.A. and Thiel, D.J., Science 263, 201–203 (1994).Google Scholar