Programming biomolecular self-assembly pathways

Nature

Volumn 451, Issue 7176, 2008, Pages 318-322

  Yin, Peng ^a,b   Choi, Harry M T ^a   Calvert, Colby R ^a   Pierce, Niles A ^a,b  

^a California Institute of Technology   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CATALYSIS; DNA; NUCLEIC ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ATOMIC FORCE MICROSCOPY; GEL ELECTROPHORESIS; GENE TECHNOLOGY; GENETIC ENGINEERING; KINETICS; LOCOMOTION; MOLECULAR DYNAMICS; MOLECULAR HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

EID: 38349121586     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature06451     Document Type: Article

References (32)

1. Butterfoss, G. L. & Kuhlman, B. Computer-based design of novel protein structures. Annu. Rev. Biophys. Biomol. Struct. 35, 49-65 (2006).
2. Seeman, N. C. DNA in a material world. Nature 421, 427-431 (2003).
3. Turberfield, A. J. et al. DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003).
4. Bois, J. S. et al. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res. 33, 4090-4095 (2005).
5. Green, S. J., Lubrich, D. & Turberfield, A. J. DNA hairpins: Fuel for autonomous DNA devices. Biophys. J. 91, 2966-2975 (2006).
6. Seelig, G., Yurke, B. & Winfree, E. Catalyzed relaxation of a metastable DNA fuel. J. Am. Chem. Soc. 128, 12211-12220 (2006).
7. Dirks, R. M. & Pierce, N. A. Triggered amplification by hybridization chain reaction. Proc. Natl Acad. Sci. USA 101, 15275-15278 (2004).
8. Rothemund, P. W. K., Papadakis, N. & Winfree, E. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, 2041-2053 (2004).
9. Seelig, G., Soloveichik, D., Zhang, D. Y. & Winfree, E. Enzyme-free nucleic acid logic circuits. Science 314, 1585-1588 (2006).
10. Yurke, B., Turberfield, A. J., Mills, J. A. P., Simmel, F. C. & Neumann, J. L. A DNAfuelled molecular machine made of DNA. Nature 406, 605-608 (2000).
11. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-544 (1998).
12. Shih, W. M., Quispe, J. D. & Joyce, G. F. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618-621 (2004).
13. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302 (2006).
14. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237-247 (1982).
15. Feldkamp, U. & Niemeyer, C. M. Rational design of DNA nanoarchitectures. Angew. Chem. Int. Edn Engl. 45, 1856-1876 (2006).
16. Robertson, A., Sinclair, A. J. & Philp, D. Minimal self-replicating systems. Chem. Soc. Rev. 29, 141-152 (2000).
17. von Kiedrowski, G. A self-replicating hexadeoxynucleotide. Angew. Chem. Int. Edn Engl. 25, 932-935 (1986).
18. Paul, N. & Joyce, G. F. A self-replicating ligase ribozyme. Proc. Natl Acad. Sci. USA 99, 12733-12740 (2002).
19. Levy, M. & Ellington, A. D. Exponential growth by cross-catalytic cleavage of deoxyribozymogens. Proc. Natl Acad. Sci. USA 100, 6416-6421 (2003).
20. Lee, D. H., Granja, J. R., Martinez, J. A., Severin, K. & Ghadiri, M. R. A self-replicating peptide. Nature 382, 525-528 (1996).
21. Zhang, D. Y., Turberfield, A. J., Yurke, B. & Winfree, E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121-1125 (2007).
22. Li, Y. et al. Controlled assembly of dendrimer-like DNA. Nature Mater. 3, 38-42 (2004).
23. Yin, P., Yan, H., Daniell, X. G., Turberfield, A. J. & Reif, J. H. A unidirectional DNA walker that moves autonomously along a track. Angew. Chem. Int. Edn Engl. 43, 4906-4911 (2004).
24. Tian, Y., He, Y., Chen, Y., Yin, P. & Mao, C. A. DNAzyme that walks processively and autonomously along a one-dimensional track. Angew. Chem. Int. Edn Engl. 44, 4355-4358 (2005).
25. Bath, J., Green, S. J. & Turberfield, A. J. A free-running DNA motor powered by a nicking enzyme. Angew. Chem. Int. Edn Engl. 44, 4358-4361 (2005).
26. Pei, R. et al. Behavior of polycatalytic assemblies in a substrate-displaying matrix. J. Am. Chem. Soc. 128, 12693-12699 (2006).
27. Venkataraman, S., Dirks, R. M., Rothemund, P. W. K., Winfree, E.&Pierce, N. A. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnol. 2, 490-494 (2007).
28. Asbury, C. L. Kinesin: world's tiniest biped. Curr. Opin. Cell Biol. 17, 89-97 (2005).
29. Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E. & Pierce, N. A. Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev. 49, 65-88 (2007).
30. Dirks, R. M., Lin, M., Winfree, E. & Pierce, N. A. Paradigms for computational nucleic acid design. Nucleic Acids Res. 32, 1392-1403 (2004).
31. Flamm, C., Fontana, W., Hofacker, I. L. & Schuster, P. RNA folding at elementary step resolution. RNA 6, 325-338 (2000).
32. Hansma, H. G. & Laney, D. E. DNA binding to mica correlates with cationic radius: assay by atomic force microscopy. Biophys. J. 70, 1933-1939 (1996).