Developmental self-assembly of a DNA tetrahedron

ACS Nano

Volumn 8, Issue 4, 2014, Pages 3251-3259

  Sadowski, John P ^a,b   Calvert, Colby R ^d   Zhang, David Yu ^a,c   Pierce, Niles A ^d,e   Yin, Peng ^a,c  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d California Institute of Technology   (United States)

^e California Institute of Technology   (United States)

Author keywords

developmental self assembly; DNA nanotechnology; kinetic pathway control; molecular programming

Indexed keywords

COMPUTATIONAL MECHANICS; GEOMETRY; ISOTHERMS; KINETICS; MOLECULES; NANOTECHNOLOGY; REACTION INTERMEDIATES; SELF ASSEMBLY; THREE DIMENSIONAL;

COMPLEX GEOMETRIES; DNA NANOTECHNOLOGY; INTERMEDIATE STATE; ISOTHERMAL GROWTH; KINETIC PATHWAY; KINETICALLY CONTROLLED; MOLECULAR PROGRAMMING; THREE DIMENSIONAL GEOMETRY;

DNA;

DNA; NANOMATERIAL;

CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; KINETICS; NANOTECHNOLOGY; PROCEDURES;

DNA; KINETICS; MODELS, MOLECULAR; NANOSTRUCTURES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION;

EID: 84899415157     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn4038223     Document Type: Article

References (46)

1. Seeman, N. C. Nucleic Acid Junctions and Lattices J. Theor. Biol. 1982, 99, 237-247
2. Seeman, N. C. DNA in a Material World Nature 2003, 421, 427-431
3. Shih, W. M.; Lin, C. Knitting Complex Weaves with DNA Origami Curr. Opin. Struct. Biol. 2010, 20, 276-282
4. Schulman, R.; Winfree, E. Synthesis of Crystals with a Programmable Kinetic Barrier to Nucleation Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 15236-15241
5. Yin, P.; Hariadi, R.; Sahu, S.; Choi, H. M. T.; Park, S. H.; LaBean, T. H.; Reif, J. H. Programming Molecular Tube Circumferences Science 2008, 321, 824-826
6. Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires Science 2003, 301, 1882-1884
7. Winfree, E.; Liu, F.; Wenzler, L. A.; Seeman, N. C. Design and Self-Assembly of Two-Dimensional DNA Crystals Nature 1998, 394, 539-544
8. Yan, H.; LaBean, T. H.; Feng, L.; Reif, J. H. Directed Nucleation Assembly of DNA Tile Complexes for Barcode-Patterned Lattices Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 8103-8108
9. Liu, D.; Wang, M.; Deng, Z.; Walulu, R.; Mao, C. Tensegrity: Construction of Rigid DNA Triangles with Flexible Four-Arm DNA Junctions J. Am. Chem. Soc. 2004, 126, 2324-2325
10. Rothemund, P. W. K.; Papadakis, N.; Winfree, E. Algorithmic Self-Assembly of DNA Sierpinski Triangles PLoS Biol. 2004, 2, 2041-2053
11. Zheng, J. P.; Birktoft, J.; Chen, Y.; Wang, T.; Sha, R. J.; Constantinou, P.; Ginell, S.; Mao, C. D.; Seeman, N. C. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal Nature 2009, 461, 74-77
12. Chen, J.; Seeman, N. C. The Synthesis from DNA of a Molecule with the Connectivity of a Cube Nature 1991, 350, 631-633
13. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
14. He, Y.; Ye, T.; Su, M.; Zhang, C.; Ribbe, A. E.; Jiang, W.; Mao, C. Hierarchical Self-Assembly of DNA into Symmetric Supramolecular Polyhedra Nature 2008, 452, 198-201
15. Douglas, S. M.; Dietz, H.; Liedl, T.; Högberg, B.; Graf, F.; Shih, W. M. Self-Assembly of DNA into Nanoscale Three-Dimensional Shapes Nature 2009, 459, 414-418
16. Dietz, H.; Douglas, S. M.; Shih, W. M. Folding DNA into Twisted and Curved Nanoscale Shapes Science 2009, 325, 725-730
17. Han, D.; Pal, S.; Nangreave, J.; Deng, Z.; Liu, Y.; Yan, H. DNA Origami with Complex Curvatures in Three-Dimensional Space Science 2011, 332, 342-346
18. Wei, B.; Dai, M.; Yin, P. Complex Shapes Self-Assembled from Single-Stranded DNA Tiles Nature 2012, 485, 623-626
19. Ke, Y.; Ong, L.; Shih, W.; Yin, P. Three-Dimensional Structures Self-Assembled from DNA Bricks Science 2012, 338, 1177-1183
20. Sobczak, J.; Martin, T.; Gerling, T.; Dietz, H. Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature Science 2012, 338, 1458-1461
21. Han, D.; Pal, S.; Yang, Y.; Jiang, S.; Nangreave, J.; Liu, Y.; Yan, H. DNA Gridiron Nanostructures Based on Four-Arm Junctions Science 2013, 339, 1412-1415
22. Zhang, D. Y.; Seelig, G. Dynamic DNA Nanotechnology Using Strand-Displacement Reactions Nature Chem. 2011, 3, 103-113
23. Bath, J.; Turberfield, A. J. DNA Nanomachines Nat. Nanotechnol. 2007, 2, 275-284
24. Yurke, B.; Turberfield, A. J.; Mills, A. P.; Simmel, F. C.; Neumann, J. L. A DNA-Fuelled Molecular Machine Made of DNA Nature 2000, 406, 605-608
25. Yan, H.; Zhang, Z.; Shen, X.; Seeman, N. C. A Robust DNA Mechanical Device Controlled by Hybridization Topology Nature 2002, 415, 62-65
26. Seelig, G.; Soloveichik, D.; Zhang, D. Y.; Winfree, E. Enzyme-Free Nucleic Acid Logic Circuits Science 2006, 314, 1585-1588
27. Zhang, D.; Turberfield, A.; Yurke, B.; Winfree, E. Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA Science 2007, 318, 1121-1125
28. Yin, P.; Choi, H. M. T.; Calvert, C. R.; Pierce, N. A. Programming Biomolecular Self-Assembly Pathways Nature 2008, 451, 318-322
29. Qian, L.; Winfree, E. Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades Science 2011, 332, 1196-1201
30. Dirks, R.; Pierce, N. Triggered Amplification by Hybridization Chain Reaction Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15275-15278
31. Venkataraman, S.; Dirks, R.; Rothemund, P.; Winfree, E.; Pierce, N. An Autonomous Polymerization Motor Powered by DNA Hybridization Nat. Nanotechnol. 2007, 2, 490-494
32. Sherman, W. B.; Seeman, N. C. A Precisely Controlled DNA Biped Walking Device Nano Lett. 2004, 4, 1203-1207
33. Shin, J.-S.; Pierce, N. A Synthetic DNA Walker for Molecular Transport J. Am. Chem. Soc. 2004, 126, 10834-10835
34. Yin, P.; Yan, H.; Daniell, X.; Turberfield, A. J.; Reif, J. A Unidirectional DNA Walker That Moves Autonomously along a Track Angew. Chem. Int. Ed. 2004, 43, 4906-4911
35. Omabegho, T.; Sha, R.; Seeman, N. C. A Bipedal DNA Brownian Motor with Coordinated Legs Science 2009, 324, 67-71
36. Nanorex, Inc. Nanoengineer-1. http://nanoengineer-1.com/ The original website is no longer available as of this writing; an archived version is available at http://web.archive.org/web/20121218/http://www.nanoengineer-1.com/ content/, accessed April 8, 2014.
37. Zhang, D. Y. Cooperative Hybridization of Oligonucleotides J. Am. Chem. Soc. 2011, 133, 1077-1086
38. Kumara, M. T.; Nykypanchuk, D.; Sherman, W. B. Assembly Pathway Analysis of DNA Nanostructures and the Construction of Parallel Motifs Nano Lett. 2008, 8, 1971-1977
39. Snyder, T. M.; Liu, D. R. Ordered Multistep Synthesis in a Single Solution Directed by DNA Templates Angew. Chem. Int. Ed. 2005, 44, 7379-7382
40. Shih, W.; Quispe, J.; Joyce, G. A 1.7-Kilobase Single-Stranded DNA That Folds into a Nanoscale Octahedron Nature 2004, 427, 618-621
41. Goodman, R.; Schaap, I.; Tardin, C.; Erben, C.; Berry, R.; Schmidt, C.; Turberfield, A. Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication Science 2005, 310, 1661-1665
42. Barish, R. D.; Schulman, R.; Rothemund, P. W. K.; Winfree, E. An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6054-6059
43. Woods, D.; Chen, H.-L.; Goodfriend, S.; Dabby, N.; Winfree, E.; Yin, P. Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time. In ITCS 2013: Innovations in Theoretical Computer Science; Association for Computing Machinery: Berkeley, CA, 2013; pp 353-354.
44. Zhang, D. Y. Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions Lect. Notes Comput. Sci. 2011, 6518, 162-175
45. Dirks, R. M.; Bois, J. S.; Schaeffer, J. M.; Winfree, E.; Pierce, N. A. Thermodynamic Analysis of Interacting Nucleic Acid Strands SIAM Rev. 2007, 49, 65-88
46. Zadeh, J. N.; Steenberg, C. D.; Bois, J. S.; Wolfe, B. R.; Pierce, M. B.; Khan, A. R.; Dirks, R. M.; Pierce, N. A. NUPACK: Analysis and Design of Nucleic Acid Systems J. Comput. Chem. 2011, 32, 170-173