Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage

Nature Communications

Volumn 5, Issue , 2014, Pages

  Hao, Chenhui ^a   Li, Xiang ^a   Tian, Cheng ^a   Jiang, Wen ^b   Wang, Guansong ^c   Mao, Chengde ^a  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c Xinqiao Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

NANOCAGE; RNA NANOCAGE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; NANOMATERIAL; VIRUS RNA;

BACTERIOPHAGE; CHEMICAL REACTION; NANOTECHNOLOGY; RNA;

ARTICLE; BACTERIOPHAGE; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; LIGHT SCATTERING; NANOENGINEERING; NATIVE POLYACRYLAMIDE GEL ELECTROPHORESIS; NONHUMAN; RNA PACKAGING; RNA STABILITY; RNA STRUCTURE; BACILLUS PHAGE; CHEMISTRY; GENETICS; NUCLEOTIDE MOTIF; VIRUS ASSEMBLY;

BACILLUS PHAGES; NANOSTRUCTURES; NUCLEOTIDE MOTIFS; RNA, VIRAL; VIRUS ASSEMBLY;

EID: 84901275902     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms4890     Document Type: Article

References (37)

1. Gesteland, R. F., Atkins, J. F. & Cech, T. R. RNA World 3rd edn (Cold Spring Harbor Laboratory Press, 2006).
2. Butcher, S. E. & Pyle, A. M. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc. Chem. Res. 44, 1302-1311 (2011).
3. Guo, P. The emerging field of RNA nanotechnology. Nat. Nanotechnol. 5, 833-842 (2010).
4. Jaeger, L. & Leontis, N. B. Tecto-RNA: one-dimensional self-assembly through tertiary interactions. Angew. Chem. Int. Ed. 39, 2521-2524 (2000). (Pubitemid 30602533)
5. Chworos, A. et al. Building programmable jigsaw puzzles with RNA. Science 306, 2068-2072 (2004). (Pubitemid 40007653)
6. Severcan, I. et al. A polyhedron made of tRNAs. Nat. Chem. 2, 772-779 (2010).
7. Afonin, K. A. et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat. Nanotechnol. 5, 676-682 (2010).
8. Dibrov, S. M., Mclean, J., Parsons, J. & Hermann, T. Self-assembling RNA square. Proc. Natl Acad. Sci. USA 108, 6405-6408 (2011).
9. Ko, S. H. et al. Synergistic self-assembly of RNA and DNA molecules. Nat. Chem. 2, 1050-1055 (2010).
10. Ohno, H. et al. Synthetic RNA-protein complex shaped like an equilateral triangle. Nat. Nanotechnol. 6, 116-120 (2011).
11. Bindewald, E., Afonin, K., Jaeger, L. & Shapiro, B. A. Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots. ACS Nano 5, 9542-9551 (2011).
12. Shu, D., Moll, W. D., Deng, Z., Mao, C. & Guo, P. Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology. Nano Lett. 4, 1717-1723 (2004). (Pubitemid 39297452)
13. Shu, Y. et al. Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs. RNA 19, 767-777 (2013).
14. Nakashima, Y., Abe, H., Abe, N., Aikawa, K. & Ito, Y. Branched RNA nanostructures for RNA interference. Chem. Commun. 47, 8367-8369 (2011).
15. Chang, C. I. et al. Enhanced intracellular delivery and multi-target gene silencing triggered by tripodal RNA structures. J. Gene Med. 14, 138-146 (2012).
16. Afonin, K. A. et al. Co-transcriptional assembly of chemically modified RNA Nanoparticles functionalized with siRNAs. Nano Lett. 12, 5192-5195 (2012).
17. Delebecque, C. J., Lindner, A. B., Silver, P. A. & Aldaye, F. A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470-474 (2011).
18. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65-87 (2010).
19. Lin, C., Liu, Y., Rinker, S. & Yan, H. DNA tile based self-assembly: Building complex nano-architectures. Chem. Phy. Chem. 7, 1641-1647 (2006).
20. Aldaye, F. A., Palmer, A. L. & Sleiman, H. F. Assembling materials with DNA as the guide. Science 321, 1795-1799 (2008).
21. Rothemund, P. W. K. Scaffolded DNA origami for nanoscale shapes and patterns. Nature 440, 297-302 (2006).
22. Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623-626 (2012).
23. Guo, P., Erickson, S. & Anderson, D. A small viral RNA is required for in vitro packaging of bacteriophage φ29 DNA. Science 236, 690-694 (1987). (Pubitemid 17076855)
24. Guo, P., Zhang, C., Chen, C., Garver, K. & Trottier, M. Inter-RNA interaction of phage φ29 pRNA to form a hexameric complex for viral DNA transportation. Mol. Cell 2, 149-155 (1998). (Pubitemid 128378977)
25. Zhang, F. et al. Function of hexameric RNA in packaging of bacteriophage phi29 DNA in vitro. Mol. Cell 2, 141-147 (1998). (Pubitemid 128378976)
26. Zhang, X. et al. Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. J. Am. Chem. Soc. 134, 2644-2652 (2012).
27. Ding, F. et al. Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. P. Natl Acad. Sci. USA 108, 7357-7362 (2011).
28. Simpson, A. A. et al. Structure of the bacteriophage φ29 DNA packaging motor. Nature 408, 745-750 (2000). (Pubitemid 32015993)
29. Shu, Y., Shu, D., Haque, F. & Guo, P. Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat. Protoc. 8, 1635-1659 (2013).
30. Guo, P., Shu, Y., Binzel, D. & Cinier, M. Synthesis, conjugation, and labeling of multifunctional pRNA nanoparticles for specific delivery of siRNA, drugs, and other therapeutics to target cells. Methods Mol. Biol. 928, 197-219 (2012).
31. Shu, D., Shu, Y., Haque, F., Abdelmawla, S. & Guo, P. Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat. Nanotechnol. 6, 658-667 (2011).
32. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671-675 (2012).
33. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38-46 (2007). (Pubitemid 44880785)
34. Goddard, T. D., Huang, C. C. & Ferrin, T. E. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157, 281-287 (2007). (Pubitemid 44880787)
35. Koyfman, A. Y. et al. Controlled spacing of cationic gold nanoparticles by nanocrown RNA. J. Am. Chem. Soc. 127, 11886-11887 (2005). (Pubitemid 41233684)
36. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (2004). (Pubitemid 41742764)
37. Deng, N. & Cieplak, P. Molecular dynamics and free energy study of the conformational equilibria in the UUUU RNA hairpin. J. Chem. Theory Comput. 3, 1435-1450 (2007).