Building programmable jigsaw puzzles with RNA

Science

Volumn 306, Issue 5704, 2004, Pages 2068-2072

  Chworos, Arkadiusz ^a   Severcan, Isil ^a   Koyfman, Alexey Y ^a   Weinkam, Patrick ^a,b   Oroudjev, Emin ^a   Hansma, Helen G ^a   Jaeger, Luc ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; HIERARCHICAL SYSTEMS; MOLECULAR STRUCTURE; SELF ASSEMBLY; SUPRAMOLECULAR CHEMISTRY; SYNTHESIS (CHEMICAL);

JIGSAW PUZZLES; NANOSCOPIC FABRICS; RNA BUILDING BLOCKS; THREE-DIMENSIONAL STRUCTURE;

RNA;

RNA;

BIOCHEMISTRY; RNA;

ARTICLE; GEOMETRY; PREDICTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN MOTIF; RNA STRUCTURE; RNA SYNTHESIS; SUPRAMOLECULAR CHEMISTRY;

ALGORITHMS; BASE SEQUENCE; CHEMISTRY, PHYSICAL; DIMERIZATION; MAGNESIUM; MICROSCOPY, ATOMIC FORCE; NANOSTRUCTURES; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; RNA; RNA, RIBOSOMAL; TEMPERATURE; THERMODYNAMICS;

EID: 10844257474     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1104686     Document Type: Article

References (36)

1. N. C. Seeman, Nature 421, 427 (2003).
2. W. M. Shih, J. D. Quispe, G. F. Joyce, Nature 427, 618 (2004).
3. C. Mao, W. Sun, N. C. Seeman, Nature 386, 137 (1997).
4. E. Winfree, F. Liu, L. A. Wenzler, N. C. Seeman, Nature 394, 539 (1998).
5. H. Yan, S. H. Park, G. Finkelstein, J. H. Reif, T. H. LaBean, Science 301, 1882 (2003).
6. H. Yan, T. H. LaBean, L. Feng, J. H. Reif. Proc. Natl. Acad. Sci. U.S.A. 100, 8103 (2003).
7. C. Mao, W. Sun, Z. Shen, N. C. Seeman, Nature 397, 144 (1999).
8. B. Yurke, A. J. Turberfield, A. P. Mills Jr., F. C. Simmel, J. L. Neumann, Nature 406, 605 (2000).
9. H. Yan, X. Zhang, Z. Shen, N. C. Seeman, Nature 415, 62 (2002).
10. E. Winfree, J. Biomol. Struct. Dyn. Conversat. 11, 263 (2000).
11. R. T. Batey, R. P. Rambo, J. A. Doudna, Angew. Chem. Int. Ed. Engl. 38, 2326 (1999).
12. N. Ban, P. Nissen, J. Hansen, P. B. Moore, T. A. Steitz, Science 289, 905 (2000).
13. B. T. Wimberly et al., Nature 407, 327 (2000).
14. F. Schluenzen et al., Cell 102, 615 (2000).
15. E. Westhof, B. Masquida, L. Jaeger, Fold. Des. 1, R78 (1996).
16. L. Jaeger, N. B. Leontis, Angew. Chem. Int. Ed. Engl. 39, 2521 (2000).
17. L. Jaeger, E. Westhof, N. B. Leontis, Nucleic Acids Res. 29, 455 (2001).
18. Y. Ikawa, K. Fukada, S. Watanabe, H. Shiraishi, T. Inoue, Structure (Cambridge) 10, 527 (2002).
19. S. Horiya et al., Chem. Biol. 10, 645 (2003).
20. B. Liu, S. Baudrey, L. Jaeger, G. C. Bazan, J. Am. Chem. Soc. 126, 4076 (2004).
21. Materials and methods are available as supporting material on Science Online.
22. E. Ennifar, P. Walter, B. Ehresmann, C. Ehresmann, P. Dumas, Nature Struct. Biol. 8, 1064 (2001).
23. 4 tectosquares.
24. R. M. Dirks, M. Lin, E. Winfree, N. A. Pierce, Nucleic Acids Res. 32, 1392 (2004).
25. A. A. Szewczak, E. R. Podell, P. C. Bevilacqua, T. R. Cech, Biochemistry 37, 11162 (1998).
26. J. S. Lodmell, C. Ehresmann, B. Ehresmann, R. Marquet, J. Mol. Biol. 311, 475 (2001).
27. H. G. Hansma, E. Oroudjev, S. Baudrey, L. Jaeger, J. Microsc. 212, 273 (2003).
28. LTs associate better when tails are oriented parallel to their a-d and b-c sides. This fact supports our twofold symmetrical models (Fig. 1C; fig. S1), with a-d and b-c being parallel to each other and a-b and c-d being tilted. Assembly through tails oriented parallel to a-b and c-d is nevertheless possible.
29. With 12 different tail-tail connectors, we are presently able to generate a 3 by 3 grid made of nine different tectosquares with the position of each of the 36 constitutive tectoRNAs being fully addressable within the RNA lattice.
30. J. Michl, T. F. Magnera, Proc. Natl. Acad. Sci. U.S.A. 99, 4788 (2002).
31. N. C. Seeman, A. M. Belcher, Proc. Natl. Acad. Sci. U.S.A. 99 (suppl. 2), 6451 (2002).
32. S. Zhang, Nature Biotechnol. 21, 1171 (2003).
33. P. Ringler, G. E. Schulz, Science 302, 106 (2003).
34. A. Carbone, N. C. Seeman, Proc. Natl. Acad. Sci. U.S.A. 99, 12577 (2002).
35. S. Wolfram, A New Kind of Science (Wolfram Media, Champaign, IL, 2002).
36. This paper is dedicated to St. Joseph, patron saint of carpenters, and to F. Michel and E. Westhof, LJ.'s mentors. Thanks to S. and L. Baudrey for technical assistance and to C. Geary, H. Waite, and S. Parsons for critical reading of the manuscript. A.C. thanks the Department of Bioorganic Chemistry, Polish Academy of Sciences, CM&MS, Lodz, 90363, Poland. Funding for this work was provided by faculty start-up funds from UCSB to LJ. and by grants from NSF to L.J. (CHE-0317154 and MRSEC DMR00-80034) and H.H. (MCB0236093).