DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles

Accounts of Chemical Research

Volumn 47, Issue 6, 2014, Pages 1881-1890

  Tan, Li Huey ^a   Xing, Hang ^a   Lu, Yi ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBOZYME; DNA; NANOPARTICLE; PROTEIN; QUANTUM DOT; STREPTAVIDIN;

CHEMISTRY; NANOTECHNOLOGY; PROCEDURES;

DNA; DNA, CATALYTIC; NANOPARTICLES; NANOTECHNOLOGY; PROTEINS; QUANTUM DOTS; STREPTAVIDIN;

EID: 84902590848     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar500081k     Document Type: Article

References (76)

1. Lu, Z.; Yin, Y. Colloidal nanoparticle clusters: functional materials by design Chem. Soc. Rev. 2012, 41, 6874-6887
2. Nie, Z.; Petukhova, A.; Kumacheva, E. Properties and emerging applications of self-assembled structures made from inorganic nanoparticles Nature Nanotech. 2010, 5, 15-25
3. Chen, X.-J.; Sanchez-Gaytan, B. L.; Qian, Z.; Park, S.-J. Noble metal nanoparticles in DNA detection and delivery Wiley Interdiscip. Rev.: Nanomed. Nanobiotechnol. 2012, 4, 273-290
4. Schroeder, A.; Heller, D. A.; Winslow, M. M.; Dahlman, J. E.; Pratt, G. W.; Langer, R.; Jacks, T.; Anderson, D. G. Treating metastatic cancer with nanotechnology Nat. Rev. Cancer 2012, 12, 39-50
5. Xia, Y.; Xiong, Y.; Lim, B.; Skrabalak, S. E. Shape-Controlled Synthesis of Metal Nanocrystals: Simple Chemistry Meets Complex Physics? Angew. Chem., Int. Ed. 2009, 48, 60-103
6. Fan, J. A.; Wu, C.; Bao, K.; Bao, J.; Bardhan, R.; Halas, N. J.; Manoharan, V. N.; Nordlander, P.; Shvets, G.; Capasso, F. Self-Assembled Plasmonic Nanoparticle Clusters Science 2010, 328, 1135-1138
7. Halas, N. J.; Lal, S.; Chang, W.-S.; Link, S.; Nordlander, P. Plasmons in Strongly Coupled Metallic Nanostructures Chem. Rev. 2011, 111, 3913-3961
8. Thomas, M. J.; Platas, A. A.; Hawley, D. K. Transcriptional Fidelity and Proofreading by RNA Polymerase II Cell 1998, 93, 627-637
9. Blanchard, S. C.; Gonzalez, R. L.; Kim, H. D.; Chu, S.; Puglisi, J. D. tRNA selection and kinetic proofreading in translation Nat. Struct. Mol. Biol. 2004, 11, 1008-1014
10. Seeman, N. C. DNA in a material world Nature 2003, 421, 427-431
11. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns Nature 2006, 440, 297-302
12. 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
13. Lo, P. K.; Karam, P.; Aldaye, F. A.; McLaughlin, C. K.; Hamblin, G. D.; Cosa, G.; Sleiman, H. F. Loading and selective release of cargo in DNA nanotubes with longitudinal variation Nature Chem. 2010, 2, 319-328
14. Pinheiro, A. V.; Han, D. R.; Shih, W. M.; Yan, H. Challenges and opportunities for structural DNA nanotechnology Nature Nanotech. 2011, 6, 763-772
15. Fu, J. L.; Liu, M. H.; Liu, Y.; Yan, H. Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures Acc. Chem. Res. 2012, 45, 1215-1226
16. Ke, Y.; Ong, L. L.; Shih, W. M.; Yin, P. Three-Dimensional Structures Self-Assembled from DNA Bricks Science 2012, 338, 1177-1183
17. Sacca, B.; Niemeyer, C. M. Functionalization of DNA nanostructures with proteins Chem. Soc. Rev. 2011, 40, 5910-5921
18. Stadler, A.; Chi, C.; van der Lelie, D.; Gang, O. DNA-incorporating nanomaterials in biotechnological applications Nanomedicine 2010, 5, 319-334
19. Li, L.-L.; Wu, P.; Hwang, K.; Lu, Y. An Exceptionally Simple Strategy for DNA-Functionalized Up-Conversion Nanoparticles as Biocompatible Agents for Nanoassembly, DNA Delivery, and Imaging J. Am. Chem. Soc. 2013, 135, 2411-2414
20. Kumar, A.; Hwang, J.-H.; Kumar, S.; Nam, J.-M. Tuning and assembling metal nanostructures with DNA Chem. Commun. 2013, 49, 2597-2609
21. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 1990, 249, 505-510
22. Ellington, A. D.; Szostak, J. W. Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures Nature 1992, 355, 850-852
23. Breaker, R. R. In Vitro Selection of Catalytic Polynucleotides Chem. Rev. 1997, 97, 371-390
24. Tan, W.; Donovan, M. J.; Jiang, J. Aptamers from Cell-Based Selection for Bioanalytical Applications Chem. Rev. 2013, 113, 2842-2862
25. Liu, J.; Cao, Z.; Lu, Y. Functional Nucleic Acid Sensors Chem. Rev. 2009, 109, 1948-1998
26. Navani, N. K.; Li, Y. Nucleic acid aptamers and enzymes as sensors Curr. Opin. Chem. Biol. 2006, 10, 272-281
27. Willner, I.; Shlyahovsky, B.; Zayats, M.; Willner, B. DNAzymes for sensing, nanobiotechnology and logic gate applications Chem. Soc. Rev. 2008, 37, 1153-1165
28. Zhang, Y.; Lu, F.; Yager, K. G.; van der Lelie, D.; Gang, O. A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems Nature Nanotech. 2013, 8, 865-872
29. Tan, S. J.; Campolongo, M. J.; Luo, D.; Cheng, W. Building plasmonic nanostructures with DNA Nature Nanotech. 2011, 6, 268-276
30. Macfarlane, R. J.; Lee, B.; Jones, M. R.; Harris, N.; Schatz, G. C.; Mirkin, C. A. Nanoparticle Superlattice Engineering with DNA Science 2011, 334, 204-208
31. Kuzyk, A.; Schreiber, R.; Fan, Z.; Pardatscher, G.; Roller, E.-M.; Hogele, A.; Simmel, F. C.; Govorov, A. O.; Liedl, T. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response Nature 2012, 483, 311-314
32. Surwade, S. P.; Zhou, F.; Wei, B.; Sun, W.; Powell, A.; O'Donnell, C.; Yin, P.; Liu, H. Nanoscale Growth and Patterning of Inorganic Oxides Using DNA Nanostructure Templates J. Am. Chem. Soc. 2013, 135, 6778-6781
33. Alivisatos, A. P.; Johnsson, K. P.; Peng, X.; Wilson, T. E.; Loweth, C. J.; Bruchez, M. P.; Schultz, P. G. Organization of 'nanocrystal molecules' using DNA Nature 1996, 382, 609-611
34. Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials Nature 1996, 382, 607-609
35. Wang, Z. D.; Lu, Y. Functional DNA directed assembly of nanomaterials for biosensing J. Mater. Chem. 2009, 19, 1788-1798
36. Sperling, R. A.; Rivera gil, P.; Zhang, F.; Zanella, M.; Parak, W. J. Biological applications of gold nanoparticles Chem. Soc. Rev. 2008, 37, 1896-1908
37. Li, L.-L.; Zhang, R.; Yin, L.; Zheng, K.; Qin, W.; Selvin, P. R.; Lu, Y. Biomimetic Surface Engineering of Lanthanide-Doped Upconversion Nanoparticles as Versatile Bioprobes Angew. Chem., Int. Ed. 2012, 51, 6121-6125
38. Mertig, M.; Ciacchi, L. C.; Seidel, R.; Pompe, W.; De Vita, A. DNA as a selective metallization template Nano Lett. 2002, 2, 841-844
39. Richards, C. I.; Choi, S.; Hsiang, J.-C.; Antoku, Y.; Vosch, T.; Bongiorno, A.; Tzeng, Y.-L.; Dickson, R. M. Oligonucleotide-Stabilized Ag Nanocluster Fluorophores J. Am. Chem. Soc. 2008, 130, 5038-5039
40. Rotaru, A.; Dutta, S.; Jentzsch, E.; Gothelf, K.; Mokhir, A. Selective dsDNA-Templated Formation of Copper Nanoparticles in Solution Angew. Chem., Int. Ed. 2010, 49, 5665-5667
41. Tikhomirov, G.; Hoogland, S.; Lee, P. E.; Fischer, A.; Sargent, E. H.; Kelley, S. O. DNA-based programming of quantum dot valency, self-assembly and luminescence Nature Nanotech. 2011, 6, 485-490
42. Choi, S.; Dickson, R. M.; Yu, J. Developing luminescent silver nanodots for biological applications Chem. Soc. Rev. 2012, 41, 1867-1891
43. Lim, D.-K.; Jeon, K.-S.; Hwang, J.-H.; Kim, H.; Kwon, S.; Suh, Y. D.; Nam, J.-M. Highly uniform and reproducible surface-enhanced Raman scattering from DNA-tailorable nanoparticles with 1-nm interior gap Nature Nanotech. 2011, 6, 452-460
44. Wang, Z.; Zhang, J.; Ekman, J. M.; Kenis, P. J. A.; Lu, Y. DNA-Mediated Control of Metal Nanoparticle Shape: One-Pot Synthesis and Cellular Uptake of Highly Stable and Functional Gold Nanoflowers Nano Lett. 2010, 10, 1886-1891
45. Wang, Z.; Tang, L.; Tan, L. H.; Li, J.; Lu, Y. Discovery of the DNA "Genetic Code" for Abiological Gold Nanoparticle Morphologies Angew. Chem., Int. Ed. 2012, 51, 9078-9082
46. Xu, L.; Kuang, H.; Xu, C.; Ma, W.; Wang, L.; Kotov, N. A. Regiospecific Plasmonic Assemblies for in Situ Raman Spectroscopy in Live Cells J. Am. Chem. Soc. 2011, 134, 1699-1709
47. Lee, J. H.; Wernette, D. P.; Yigit, M. V.; Liu, J.; Wang, Z.; Lu, Y. Site-Specific Control of Distances between Gold Nanoparticles Using Phosphorothioate Anchors on DNA and a Short Bifunctional Molecular Fastener Angew. Chem., Int. Ed. 2007, 46, 9006-9010
48. Fidanza, J. A.; Ozaki, H.; McLaughlin, L. W. Site-specific labeling of DNA sequences containing phosphorothioate diesters J. Am. Chem. Soc. 1992, 114, 5509-5517
49. Lee, J. H.; Wong, N. Y.; Tan, L. H.; Wang, Z.; Lu, Y. Controlled Alignment of Multiple Proteins and Nanoparticles with Nanometer Resolution via Backbone-Modified Phosphorothioate DNA and Bifunctional Linkers J. Am. Chem. Soc. 2010, 132, 8906-8908
50. Wong, N. Y.; Zhang, C.; Tan, L. H.; Lu, Y. Site-Specific Attachment of Proteins onto a 3D DNA Tetrahedron through Backbone-Modified Phosphorothioate DNA Small 2011, 7, 1427-1430
51. Walther, A.; Müller, A. H. E. Janus Particles: Synthesis, Self-Assembly, Physical Properties, and Applications Chem. Rev. 2013, 113, 5194-5261
52. Xu, X.; Rosi, N. L.; Wang, Y.; Huo, F.; Mirkin, C. A. Asymmetric Functionalization of Gold Nanoparticles with Oligonucleotides J. Am. Chem. Soc. 2006, 128, 9286-9287
53. Kim, J.-W.; Kim, J.-H.; Deaton, R. DNA-Linked Nanoparticle Building Blocks for Programmable Matter Angew. Chem., Int. Ed. 2011, 50, 9185-9190
54. Lee, J.-H.; Kim, G.-H.; Nam, J.-M. Directional Synthesis and Assembly of Bimetallic Nanosnowmen with DNA J. Am. Chem. Soc. 2012, 134, 5456-5459
55. Xing, H.; Wang, Z.; Xu, Z.; Wong, N. Y.; Xiang, Y.; Liu, G. L.; Lu, Y. DNA-Directed Assembly of Asymmetric Nanoclusters Using Janus Nanoparticles ACS Nano 2011, 6, 802-809
56. Tan, L. H.; Xing, H.; Chen, H.; Lu, Y. Facile and Efficient Preparation of Anisotropic DNA-Functionalized Gold Nanoparticles and Their Regioselective Assembly J. Am. Chem. Soc. 2013, 135, 17675-17678
57. Perro, A.; Reculusa, S.; Ravaine, S.; Bourgeat-Lami, E.; Duguet, E. Design and synthesis of Janus micro- and nanoparticles J. Mater. Chem. 2005, 15, 3745-3760
58. Wu, L. Y.; Ross, B. M.; Hong, S.; Lee, L. P. Bioinspired Nanocorals with Decoupled Cellular Targeting and Sensing Functionality Small 2010, 6, 503-507
59. Lu, Y.; Liu, J. Smart Nanomaterials Inspired by Biology: Dynamic Assembly of Error-Free Nanomaterials in Response to Multiple Chemical and Biological Stimuli Acc. Chem. Res. 2007, 40, 315-323
60. 2+ detection J. Am. Chem. Soc. 2004, 126, 12298-12305
61. 2+): Development and Comparison of Labeled and Label-Free DNAzyme-Gold Nanoparticle Systems J. Am. Chem. Soc. 2008, 130, 14217-14226
62. 2+ detection with a ligation DNAzyme and nanoparticles Chem. Commun. 2007, 4872-4874
63. Liu, J.; Lu, Y. Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles Angew. Chem., Int. Ed. 2006, 45, 90-94
64. Liu, J.; Lee, J. H.; Lu, Y. Quantum Dot Encoding of Aptamer-Linked Nanostructures for One-Pot Simultaneous Detection of Multiple Analytes Anal. Chem. 2007, 79, 4120-4125
65. Yim, T.-J.; Liu, J.; Lu, Y.; Kane, R. S.; Dordick, J. S. Highly Active and Stable DNAzyme-Carbon Nanotube Hybrids J. Am. Chem. Soc. 2005, 127, 12200-12201
66. Yigit, M. V.; Mazumdar, D.; Lu, Y. MRI Detection of Thrombin with Aptamer Functionalized Superparamagnetic Iron Oxide Nanoparticles Bioconjugate Chem. 2008, 19, 412-417
67. Wang, D. Y.; Lai, B. H. Y.; Sen, D. A General Strategy for Effector-mediated Control of RNA-cleaving Ribozymes and DNA Enzymes J. Mol. Biol. 2002, 318, 33-43
68. Liu, J.; Lu, Y. Adenosine-Dependent Assembly of Aptazyme-Functionalized Gold Nanoparticles and Its Application as a Colorimetric Biosensor Anal. Chem. 2004, 76, 1627-1632
69. Liu, J.; Lu, Y. Smart Nanomaterials Responsive to Multiple Chemical Stimuli with Controllable Cooperativity Adv. Mater. 2006, 18, 1667-1671
70. Liu, J.; Wernette, D. P.; Lu, Y. Proofreading and Error Removal in a Nanomaterial Assembly Angew. Chem., Int. Ed. 2005, 44, 7290-7293
71. Xiang, Y.; Wang, Z.; Xing, H.; Lu, Y. Expanding DNAzyme functionality through enzyme cascades with applications in single nucleotide repair and tunable DNA-directed assembly of nanomaterials Chem. Sci. 2013, 4, 398-404
72. Wong, N. Y.; Xing, H.; Tan, L. H.; Lu, Y. Nano-Encrypted Morse Code: A Versatile Approach to Programmable and Reversible Nanoscale Assembly and Disassembly J. Am. Chem. Soc. 2013, 135, 2931-2934
73. Kimura-Suda, H.; Petrovykh, D. Y.; Tarlov, M. J.; Whitman, L. J. Base-Dependent Competitive Adsorption of Single-Stranded DNA on Gold J. Am. Chem. Soc. 2003, 125, 9014-9015
74. Zhang, S.; Park, Y.-S.; Li, J.; Lu, X.; Zhang, W.; Zhang, X. Negative Refractive Index in Chiral Metamaterials Phys. Rev. Lett. 2009, 102, 023901
75. Wu, X.; Xu, L.; Liu, L.; Ma, W.; Yin, H.; Kuang, H.; Wang, L.; Xu, C.; Kotov, N. A. Unexpected Chirality of Nanoparticle Dimers and Ultrasensitive Chiroplasmonic Bioanalysis J. Am. Chem. Soc. 2013, 135, 18629-18636
76. Chen, Q.; Whitmer, J. K.; Jiang, S.; Bae, S. C.; Luijten, E.; Granick, S. Supracolloidal Reaction Kinetics of Janus Spheres Science 2011, 331, 199-202