Ring Catalog: A resource for designing self-assembling RNA nanostructures

Methods

Volumn 103, Issue , 2016, Pages 128-137

  Parlea, Lorena ^a   Bindewald, Eckart ^b   Sharan, Rishabh ^a   Bartlett, Nathan ^a   Moriarty, Daniel ^a   Oliver, Jerome ^a   Afonin, Kirill A ^c   Shapiro, Bruce A ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

^c UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

Author keywords

3D structural elements; Nanoconstruct; RNA motifs; RNA nanoparticle; Self assembly; Sequence design

Indexed keywords

NANOMATERIAL; NANOPARTICLE; RNA;

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; PRECIPITATION; PRIORITY JOURNAL; RNA EXTRACTION; RNA PROCESSING; RNA PURIFICATION; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; WEB BROWSER; CHEMISTRY; CONFORMATION; DIMERIZATION; NUCLEIC ACID DATABASE; SOFTWARE;

DATABASES, NUCLEIC ACID; DIMERIZATION; NANOSTRUCTURES; NUCLEIC ACID CONFORMATION; RNA; SOFTWARE;

EID: 84964680520     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.04.016     Document Type: Article

References (53)

1. Jaeger L., Westhof E., Leontis N.B. TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res. 2001, 29(2):455-463.
2. Chworos A., et al. Building programmable jigsaw puzzles with RNA. Science 2004, 306(5704):2068-2072.
3. Severcan I., et al. A polyhedron made of tRNAs. Nat. Chem. 2010, 2(9):772-779.
4. Yingling Y.G., Shapiro B.A. Computational design of an RNA hexagonal nanoring and an RNA nanotube. Nano Lett. 2007, 7(8):2328-2334.
5. Afonin K.A., et al. Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine. Nat. Protoc. 2011, 6(12):2022-2034.
6. Afonin K.A., et al. Multifunctional RNA nanoparticles. Nano Lett. 2014, 14(10):5662-5671.
7. Dao B.N., et al. Triggering RNAi with multifunctional RNA nanoparticles and their delivery. DNA RNA Nanotechnol. 2015, 1(1):27-38.
8. Feng L., et al. Ocular delivery of pRNA nanoparticles: distribution and clearance after subconjunctival injection. Pharm. Res. 2014, 31(4):1046-1058.
9. Guo P. The emerging field of RNA nanotechnology. Nat. Nanotechnol. 2010, 5(12):833-842.
10. Khaled A., et al. Controllable self-assembly of nanoparticles for specific delivery of multiple therapeutic molecules to cancer cells using RNA nanotechnology. Nano Lett. 2005, 5(9):1797-1808.
11. Khisamutdinov E.F., Jasinski D.L., Guo P. RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS Nano 2014, 8(5):4771-4781.
12. Khisamutdinov E.F., et al. Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles. Nucleic Acids Res. 2014, 42(15):9996-10004.
13. Ohno H., Inoue T. Designed regular tetragon-shaped RNA-protein complexes with ribosomal protein L1 for bionanotechnology and synthetic biology. ACS Nano 2015.
14. Ohno H., et al. Synthetic RNA-protein complex shaped like an equilateral triangle. Nat. Nanotechnol. 2011, 6(2):116-120.
15. Osada E., et al. Engineering RNA-protein complexes with different shapes for imaging and therapeutic applications. ACS Nano 2014, 8(8):8130-8140.
16. Rychahou P., et al. Delivery of RNA nanoparticles into colorectal cancer metastases following systemic administration. ACS Nano 2015, 9(2):1108-1116.
17. Shu D., et al. Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat. Nanotechnol. 2011, 6(10):658-667.
18. Shu Y., et al. Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv. Drug Deliv. Rev. 2014, 66:74-89.
19. Shu Y., et al. Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat. Protoc. 2013, 8(9):1635-1659.
20. Shukla G.C., et al. A boost for the emerging field of RNA nanotechnology. ACS Nano 2011, 5(5):3405-3418.
21. Afonin K.A., et al. In silico design and enzymatic synthesis of functional RNA nanoparticles. Acc. Chem. Res. 2014, 47(6):1731-1741.
22. Leontis N.B., Lescoute A., Westhof E. The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol. 2006, 16(3):279-287.
23. Hendrix D.K., Brenner S.E., Holbrook S.R. RNA structural motifs: building blocks of a modular biomolecule. Q. Rev. Biophys. 2005, 38(3):221-243.
24. Afonin K.A., et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat. Nanotechnol. 2010, 5(9):676-682.
25. Afonin K.A., et al. Computational and experimental characterization of RNA cubic nanoscaffolds. Methods 2014, 67(2):256-265.
26. Bida J.P., Das R. Squaring theory with practice in RNA design. Curr. Opin. Struct. Biol. 2012, 22(4):457-466.
27. Kasprzak W., et al. Use of RNA structure flexibility data in nanostructure modeling. Methods 2011, 54(2):239-250.
28. Guo P., et al. Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol. Cell 1998, 2(1):149-155.
29. Shu D., et al. Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology. Nano Lett. 2004, 4(9):1717-1723.
30. Shu Y., et al. Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs. RNA 2013, 19(6):767-777.
31. Haque F., et al. Ultrastable synergistic tetravalent RNA nanoparticles for targeting to cancers. Nano Today 2012, 7(4):245-257.
32. Bindewald E., et al. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler. J. Mol. Graph. Model. 2008, 27(3):299-308.
33. Bindewald E., et al. RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res. 2008, 36(Database issue):D392-7.
34. Lilley D.M. Structures of helical junctions in nucleic acids. Q. Rev. Biophys. 2000, 33(2):109-159.
35. Churchwell C.J., et al. The signature molecular descriptor. 3. Inverse-quantitative structure-activity relationship of ICAM-1 inhibitory peptides. J. Mol. Graph. Model. 2004, 22(4):263-273.
36. Faulon J.L., Churchwell C.J., Visco D.P. The signature molecular descriptor. 2. Enumerating molecules from their extended valence sequences. J. Chem. Inf. Comput. Sci. 2003, 43(3):721-734.
37. Faulon J.L., Collins M.J., Carr R.D. The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences. J. Chem. Inf. Comput. Sci. 2004, 44(2):427-436.
38. Faulon J.L., Visco D.P., Pophale R.S. The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies. J. Chem. Inf. Comput. Sci. 2003, 43(3):707-720.
39. Bindewald E., et al. Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots. ACS Nano 2011, 5(12):9542-9551.
40. Ren P., Wu C., Ponder J.W. Polarizable atomic multipole-based molecular mechanics for organic molecules. J. Chem. Theory Comput. 2011, 7(10):3143-3161.
41. Case D.A., et al. AMBER 2015 2015, University of California, San Francisco.
42. Rosa M.D. DNA sequence for the T7 RNA polymerase promoter for T7 RNA species II. J. Mol. Biol. 1981, 147(1):199-204.
43. Weston B.F., Kuzmine I., Martin C.T. Positioning of the start site in the initiation of transcription by bacteriophage T7 RNA polymerase. J. Mol. Biol. 1997, 272(1):21-30.
44. Grabow W.W., et al. Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. Nano Lett. 2011, 11(2):878-887.
45. Boerneke M.A., Dibrov S.M., Hermann T. Crystal-structure-guided design of self-assembling RNA nanotriangles. Angew. Chem. Int. Ed. Engl. 2016, 55(12):4097-4100.
46. Cayrol B., et al. A nanostructure made of a bacterial noncoding RNA. J. Am. Chem. Soc. 2009, 131(47):17270-17276.
47. Short F.L., et al. Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot. Proc. Natl. Acad. Sci. U.S.A. 2013, 110(3):E241-E249.
48. Chen C., Zhang C., Guo P. Sequence requirement for hand-in-hand interaction in formation of RNA dimers and hexamers to gear phi29 DNA translocation motor. RNA 1999, 5(6):805-818.
49. Boerneke M.A., et al. Functional conservation despite structural divergence in ligand-responsive RNA switches. Proc. Natl. Acad. Sci. U.S.A. 2014, 111(45):15952-15957.
50. Hadamard J. Sur les problèmes aux dérivées partielles et leur signification physique. Princeton Univ. Bull. 1902, 49-52.
51. Barnaby S.N., et al. Modular and chemically responsive oligonucleotide "bonds" in nanoparticle superlattices. J. Am. Chem. Soc. 2015, 137(42):13566-13571.
52. Davidovich C., et al. Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(11):4291-4296.
53. Leontis N.B., Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA 2001, 7(4):499-512.