Synthetic RNA-protein complex shaped like an equilateral triangle

Nature Nanotechnology

Volumn 6, Issue 2, 2011, Pages 116-120

  Ohno, Hirohisa ^a   Kobayashi, Tetsuhiro ^a   Kabata, Rinko ^a   Endo, Kei ^b   Iwasa, Takuma ^a   Yoshimura, Shige H ^a   Takeyasu, Kunio ^a   Inoue, Tan ^a,b   Saito, Hirohide ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NANOSTRUCTURES; PROTEINS; RNA; SCAFFOLDS (BIOLOGY); SYNTHETIC BIOLOGY;

BIOMACROMOLECULES; BOTTOM UP APPROACH; DNA NANOSTRUCTURES; EQUILATERAL TRIANGLES; RIBOSOMAL PROTEINS; RNA-PROTEIN COMPLEXES; WATSON-CRICK BASE PAIRING;

NUCLEIC ACIDS;

DNA; NANOMATERIAL; RIBOSOMAL PROTEIN L7AE; RIBOSOME PROTEIN; RNA; UNCLASSIFIED DRUG;

ARTICLE; DNA STRUCTURE; NANOMEDICINE; PRIORITY JOURNAL; PROTEIN BINDING; RNA STRUCTURE;

EID: 79751523855     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2010.268     Document Type: Article

References (36)

1. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65-87 (2010).
2. Lin, C., Liu, Y. & Yan, H. Designer DNA nanoarchitectures. Biochemistry 48, 1663-1674 (2009).
3. Goodman, R. P. et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661-1665 (2005). (Pubitemid 41780784)
4. Rothemund, P.W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302 (2006).
5. Andersen, E. S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73-76 (2009).
6. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414-418 (2009).
7. Rinker, S., Ke, Y., Liu, Y., Chhabra, R. & Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nature Nanotech. 3, 418-422 (2008).
8. Ke, Y., Lindsay, S., Chang, Y., Liu, Y. & Yan, H. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319, 180-183 (2008).
9. Voigt, N. V. et al. Single-molecule chemical reactions on DNA origami. Nature Nanotech. 5, 200-203 (2010).
10. Endo, M., Katsuda, Y., Hidaka, K. & Sugiyama, H. Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 132, 1592-1597 (2010).
11. Moore, T., Zhang, Y., Fenley, M. O. & Li, H. Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 12, 807-818 (2004). (Pubitemid 38595769)
12. Rozhdestvensky, T. S. et al. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res. 31, 869-877 (2003). (Pubitemid 36240424)
13. Turner, B., Melcher, S. E., Wilson, T. J., Norman, D. G. & Lilley, D. M. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. RNA 11, 1192-1200 (2005). (Pubitemid 41132391)
14. Guo, P. RNA nanotechnology: engineering, assembly and applications in detection, gene delivery and therapy. J. Nanosci. Nanotechnol. 5, 1964-1982 (2005). (Pubitemid 44874820)
15. Guo, P. The emerging field of RNA nanotechnology. Nature Nanotech. 5, 833-842 (2010).
16. Saito, H. & Inoue, T. Synthetic biology with RNA motifs. Int. J. Biochem. Cell Biol. 41, 398-404 (2009).
17. Saito, H. & Inoue, T. RNA and RNP as new molecular parts in synthetic biology. J. Biotechnol. 132, 1-7 (2007). (Pubitemid 47503387)
18. Win, M. N., Liang, J. C. & Smolke, C. D. Frameworks for programming biological function through RNA parts and devices. Chem. Biol. 16, 298-310 (2009).
19. Jaeger, L. & Chworos, A. The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol. 16, 531-543 (2006). (Pubitemid 44149075)
20. Leontis, N. B., Lescoute, A. & Westhof, E. The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol. 16, 279-287 (2006). (Pubitemid 43831653)
21. Matsumura, S., Ikawa, Y. & Inoue, T. Biochemical characterization of the kink-turn RNA motif. Nucleic Acids Res. 31, 5544-5551 (2003). (Pubitemid 37441924)
22. Lescoute, A., Leontis, N. B., Massire, C. &Westhof, E. Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acids Res. 33, 2395-2409 (2005). (Pubitemid 41511259)
23. Ikawa, Y., Tsuda, K., Matsumura, S. & Inoue, T. De novo synthesis and development of an RNA enzyme. Proc. Natl Acad. Sci. USA 101, 13750-13755 (2004). (Pubitemid 39298479)
24. Penchovsky, R. & Breaker, R. R. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnol.23, 1424-1433 (2005). (Pubitemid 41679396)
25. Voytek, S. B. & Joyce, G. F. Niche partitioning in the coevolution of 2 distinct RNA enzymes. Proc. Natl Acad. Sci. USA 106, 7780-7785 (2009).
26. Horiya, S. et al. RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions. Chem. Biol. 10, 645-654 (2003). (Pubitemid 36940941)
27. Chworos, A. et al. Building programmable jigsaw puzzles with RNA. Science 306, 2068-2072 (2004). (Pubitemid 40007653)
28. Ko, S. H., Chen, Y., Shu, D., Guo, P. & Mao, C. Reversible switching of pRNA activity on the DNA packaging motor of bacteriophage phi29. J. Am. Chem. Soc. 130, 17684-17687 (2008).
29. Severcan, I. et al. A polyhedron made of tRNAs. Nature Chem. 2, 772-779 (2010).
30. Afonin, K. A. et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nature Nanotech. 5, 676-682 (2010).
31. Saito, H. et al. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nature Chem. Biol. 6, 71-78 (2010).
32. Goody, T. A., Melcher, S. E., Norman, D. G. & Lilley, D. M. The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA 10, 254-264 (2004). (Pubitemid 38129830)
33. Service, R. F. Materials and biology. Nanotechnology takes aim at cancer. Science 310, 1132-1134 (2005). (Pubitemid 41681730)
34. Holler, N. et al. Two adjacent trimeric Fas ligands are required for Fas signaling and formation of a death-inducing signaling complex. Mol. Cell. Biol. 23, 1428-1440 (2003). (Pubitemid 36177050)
35. Ranzinger, J. et al. Nanoscale arrangement of apoptotic ligands reveals a demand for a minimal lateral distance for efficient death receptor activation. Nano Lett. 9, 4240-4245 (2009).
36. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 resolution. Science 289, 905-920 (2000). (Pubitemid 30659939)