Design and self-assembly of two-dimensional DNA crystals

Nature

Volumn 394, Issue 6693, 1998, Pages 539-544

  Winfree, Erik ^a   Liu, Furong ^b   Wenzler, Lisa A ^b   Seeman, Nadrian C ^b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATOMIC FORCE MICROSCOPY; CROSSING OVER; DIAGNOSTIC APPROACH ROUTE; DNA STRUCTURE; DNA SYNTHESIS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY;

BASE SEQUENCE; CRYSTALLIZATION; DNA; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MICROSCOPY, ATOMIC FORCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; SURFACE PROPERTIES;

EID: 0032490948     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/28998     Document Type: Article

References (40)

1. Liu, B., Leontis, N. B. & Seeman, N. C. Bulged 3-arm DNA branched junctions as components for nanoconstruction. Nanobiology 3, 177-188 (1994).
2. Seeman, N. C. Nucleic-acid junctions and lattices. J. Theor. Biol. 99, 237-247 (1982).
3. Cohen, S. N., Chang, A. C. Y., Boyer, H. W. & Helling, R. B. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl Acad. Sci. USA 70, 3240-3244 (1973).
4. Qiu, H., Dewan, J. & Seeman, N. C. A DNA decamer with a sticky end: The crystal structure of d-CGACGATCGT. J. Mol. Biol. 267, 881-898 (1997).
5. Ma, R.-I., Kallenbach, N. R., Sheardy, R. D., Petrillo, M. L. & Seeman, N. C. Three-arm nucleic acid junctions are flexible. Nucleic Acids Res. 14, 9745-9753 (1986).
6. Petrillo, M. L. et al. The ligation and flexibility of four-arm DNA junctions. Biopolymers V, 1337-1352 (1988).
7. Fu, T.-J. & Seeman, N. C. DNA double-crossover molecules. Biochemistry 32, 3211-3220 (1993).
8. Schwacha, A. & Kleckner, N. Identification of double Holliday junctions as intermediates in meiotic recombination. Cell 83, 783-791 (1995).
9. Li, X., Yang, X., Qi, I. & Seeman, N. C. Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Am. Chem. Soc. 118, 6131-6140 (1996).
10. Winfree, E. in DNA Based Computers: Proceedings of a DIMACS Workshop, April 4, 1995, Princeton University (eds Lipton, R. J. & Baum, E. B.) 199-221 (American Mathematical Society, Providence, RI, 1996).
11. Adleman, L. M. Molecular computation of solutions to combinatorial problems. Science 266, 1021-1024 (1994).
12. Grünbaum, B. & Shephard, G. C. Tilings and Patterns (Freeman, New York, 1986).
13. Wang, H. in Proc. Symp. Math. Theory of Automata 23-56 (Polytechnic, New York, 1963).
14. Winfree, E., Yang, X. & Seeman, N. C. in Proceedings of the 2nd DIMACS Meeting on DNA Based Computers, Princeton University, June 20-12, 1996 (American Mathematical Society, Providence, RJ, in the press).
15. Reif, J. in Proceedings of the 3rd DIMACS Meeting on DNA Based Computers, University of Pennsylvania, June 23-25, 1997 (American Mathematical Society, Providence, RI, in the press).
16. Binnig, G., Quate, C. F. & Gerber, C. Atomic force microscope. Phys. Rev. Lett. 56, 930-933 (1986).
17. Wang, I. C. Helical repeat of DNA in solution. Proc. Natl Acad. Sci. USA 76, 200-203 (1979).
18. Rhodes, D. & Klug, A. Helical periodicity of DNA determined by enzyme digestion. Nature 286, 573-578 (1980).
19. Seeman, N. C. De novo design of sequences for nucleic acid structural engineering. J. Biomol. Struct. Dyns 8, 573-581 (1990).
20. Yue, K. & Dill, K. A. Inverse protein folding problem - designing polymer sequences. Proc. Natl Acad. Sci. USA 89, 4163-4167 (1992).
21. Sun, S., Brem, R., Chan, H. S. & Dill, K. A. Designing amino acid sequences to fold with good hydrophobic cores. Prot. Engng 9, 1205-1213 (1996).
22. SantaLucia, I., Allawi, H. T. & Seneviratne, A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555-3562 (1996).
23. Ouporov, I. V. & Leontis, N. B. Refinement of the solution structure of a branched DNA three-way junction. Biophys. J. 68, 266-274 (1995).
24. Hansma, H. G. et al. Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope. Science 256, 1180-1184 (1992).
25. Shaiu, W.-L., Larson, D. D., Vesenka, J. & Henderson, E. Atomic force microscopy of oriented linear DNA molecules labelled with 5 nm gold spheres. Nucleic Acids Res. 21, 99-103 (1993).
26. Shaiu, W.-L., Vesenka, J., Jondle, D., Henderson, E. & Larson, D. D. Visualization of circular DNA molecules labelled with colloidal gold spheres using atomic force microscopy. J. Vac. Sci. Tech. A 11, 820-823 (1993).
27. Whitesides, G. M., Mathias, I. P. & Seto, C. T. Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. Science 254, 1312-1319 (1991).
28. Niemeyer, C. M., Sano, T., Smith, C. L. & Cantor, C. R. Oligonucleotide-directed self-assembly of proteins. Nucleic Acids Res. 22, 5530-5539 (1994).
29. Alivisatos, A. P. et al. Organization of 'nanocrystal molecules' using DNA. Nature 382, 609-611 (1996).
30. Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, I. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607-609 (1996).
31. Braun, E., Eichen, Y., Sivan, U. & Ben-Yoseph, G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature 391, 775-778 (1998).
32. Breaker, R. R. & Joyce, G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229 (1994).
33. Chen, J. & Seeman, N. C. The synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631-633 (1991).
34. Zhang, Y. & Seeman, N. C. The construction of a DNA truncated octahedron. J. Am. Chem. Soc. 116, 1661-1669 (1994).
35. Joannopolous, J. D., Meade, R. D. & Winn, J. N. Photonic Crystals: Moulding the Flow of Light (Princeton University Press, Princeton, 1995).
36. Ribeiro, F. R. et al. Structure-activity relationships in zeolites. J. Mol. Cat. A: Chem. 96, 245-270 (1996).
37. Robinson, B. H. & Seeman, N. C. The design of a biochip: A self-assembling molecular-scale memory device. Prot. Engng 1, 295-300 (1987).
38. Haddon, R. C. & Lamola, A. A. The molecular electronic defice and the biochip computer: present status. Proc. Natl Acad. Sci. USA 82, 1874-1878 (1985).
39. Carter, E. S. & Tung, C.-S. NAMOT2 - a redesigned nucleic acid modelling tool: construction of non-canonical DNA structures. CABIOS 12, 25-30 (1996).
40. Vainshtein, B. K. Modern Crystallography, 1: Fundamentals of Crystals (Springer, New York, 1994).