Single-molecule analysis using DNA origami

Angewandte Chemie - International Edition

Volumn 51, Issue 4, 2012, Pages 874-890

  Rajendran, Arivazhagan ^a   Endo, Masayuki ^b,c   Sugiyama, Hiroshi ^a,c  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

atomic force microscopy; DNA origami; nanodevices; nanotechnology; single molecule studies

Indexed keywords

ANALYTICAL TECHNIQUES; ATTACHMENT POINTS; BIOCHEMICAL PROCESS; BIOCHEMICAL REACTIONS; DNA NANOTECHNOLOGY; FUTURE DIRECTIONS; HIGH-THROUGHPUT; LAB-ON-A-CHIP SYSTEMS; NANO-DEVICES; NANO-OBJECTS; PRECISE POSITIONING; RECENT PROGRESS; SALIENT FEATURES; SINGLE-MOLECULE; SINGLE-MOLECULE ANALYSIS; SINGLE-MOLECULE STUDIES;

ATOMIC FORCE MICROSCOPY; BIOASSAY; BIOCHEMISTRY; BIOCHIPS; DNA; MOLECULES; NANOTECHNOLOGY;

CHEMICAL ANALYSIS;

APTAMER; DNA; DNA TOPOISOMERASE; GUANINE QUADRUPLEX; PROTEIN;

CHEMISTRY; CLICK CHEMISTRY; HUMAN; LAB ON A CHIP; METABOLISM; NANOTECHNOLOGY; PROTEIN BINDING; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

APTAMERS, NUCLEOTIDE; CLICK CHEMISTRY; DNA; DNA TOPOISOMERASES, TYPE I; G-QUADRUPLEXES; HUMANS; LAB-ON-A-CHIP DEVICES; NANOTECHNOLOGY; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; PROTEINS;

EID: 84856020756     PISSN: 14337851     EISSN: 15213773     Source Type: Journal    
DOI: 10.1002/anie.201102113     Document Type: Review

References (116)

1. C. Bustamante, Q. Rev. Biophys. 2005, 38, 291-301
2. C. Bustamante, Annu. Rev. Biochem. 2008, 77, 45-50.
3. P. V. Cornish, T. Ha, ACS Chem. Biol. 2007, 2, 53-61.
4. J. R. Kuhn, T. D. Pollard, J. Biol. Chem. 2007, 282, 28014-28024
5. J. Park, Y. Jeon, D. In, R. Fishel, C. Ban, J-B. Lee, PLoS One 2010, 5, e 15496.
6. A. Camacho, K. Korn, M. Damond, J.-F. Cajot, E. Litborn, B. Liao, P. Thyberg, H. Winter, A. Honegger, P. Gardellin, R. Rigler, J. Biotechnol. 2004, 107, 107-114
7. J. Hasse, J. Jacak, M. Kasper, G. Regl, T. Eichberger, M. Winklmayr, F. Aberger, M. Sonnleitner, R. Schlapak, S. Howorka, L. Muresan, A-;M. Frischauf, G. J. Schutz, Genome Res. 2006, 16, 1041-1045
8. K. Korn, P. Gardellin, B. Liao, M. Amacker, A. Bergstrom, H. Bjorkman, A. Camacho, S. Dorhofer, K. Dorre, J. Enstrom, T. Ericson, T. Favez, M. Gosch, A. Honegger, S. Jaccoud, M. Lapczyna, E. Litborn, P. Thyberg, H. Winter, R. Rigler, Nucleic Acids Res. 2003, 31, e 89.
9. C. R. Twist, M. K. Winson, J. J. Rowland, D. B. Kell, Anal. Biochem. 2004, 327, 35-44
10. P.-Y. Kwok, M. Xiao, Hum. Mutat. 2004, 23, 442-446.
11. J. Sung, S. Sivaramakrishnan, A. R. Dunn, J. A. Spudich, Methods Enzymol. 2010, 475, 321-375
12. T. B. Miranda, T. K. Kelly, K. Bouazoune, P. A. Jones, Curr. Protoc. Mol. Biol. 2010, 89, 21.17.1- 21.17.16.
13. M. Hintersteiner, M. Auer, Ann. N. Y. Acad. Sci. 2008, 1130, 1-11
14. G. M. Skinner, K. Visscher, Assay Drug Dev. Technol. 2004, 2, 397-406.
15. D. Schomburg, I. Schomburg, Springer Handbook of Enzymes, 2nd ed., Springer, New York, 2001.
16. M. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craighead, W. W. Webb, Science 2003, 299, 682-686.
17. N. C. Seeman, J. Theor. Biol. 1982, 99, 237-247.
18. K. Lund, Y. Liu, S. Lindsay, H. Yan, J. Am. Chem. Soc. 2005, 127, 17606-17607
19. S. H. Park, C. Pistol, S. J. Ahn, J. H. Reif, A. R. Lebeck, C. Dwyer, T. H. LaBean, Angew. Chem. 2006, 118, 749-753
20. Angew. Chem. Int. Ed. 2006, 45, 735-739
21. A. Chworos, I. Severcan, A. Y. Koyfman, P. Weinkam, E. Oroudjev, H. G. Hansma, L. Jaeger, Science 2004, 306, 2068-2072.
22. M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 2010, 132, 1592-1597.
23. X. D. Cheng, Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 293-318
24. B. Youngblood, N. O. Reich, J. Biol. Chem. 2006, 281, 26821-26831.
25. P. W. K. Rothemund, Nature 2006, 440, 297-302.
26. Z. Zhao, H. Yan, Y. Liu, Angew. Chem. 2010, 122, 1456-1459
27. Angew. Chem. Int. Ed. 2010, 49, 1414-1417
28. A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, ACS Nano 2011, 5, 665-671
29. M. Endo, T. Sugita, A. Rajendran, Y. Katsuda, T. Emura, K. Hidaka, H. Sugiyama, Chem. Commun. 2011, 47, 3213-3215
30. W. Liu, H. Zhong, R. Wang, N. C. Seeman, Angew. Chem. 2011, 123, 278-281
31. Angew. Chem. Int. Ed. 2011, 50, 264-267.
32. E. S. Andersen, M. Dong, M. M. Nielsen, K. Jahn, R. Subramani, W. Mamdouh, M. M. Golas, B. Sander, H. Stark, C. L. P. Oliveira, J. S. Pedersen, V. Birkedal, F. Besenbacher, K. V. Gothelf, J. Kjems, Nature 2009, 459, 73-76
33. A. Kuzuya, M. Komiyama, Chem. Commun. 2009, 4182-4184
34. Y. Ke, J. Sharma, M. Liu, K. Jahn, Y. Liu, H. Yan, Nano Lett. 2009, 9, 2445-2447
35. M. Endo, K. Hidaka, T. Kato, K. Namba, H. Sugiyama, J. Am. Chem. Soc. 2009, 131, 15570-15571
36. M. Endo, K. Hidaka, H. Sugiyama, Org. Biomol. Chem. 2011, 9, 2075-2077
37. S. M. Douglas, H. Dietz, T. Liedl, B. Hogberg, F. Graf, W. M. Shih, Nature 2009, 459, 414-418
38. H. Dietz, S. M. Douglas, W. M. Shih, Science 2009, 325, 725-730
39. Y. Ke, S. M. Douglas, M. Liu, J. Sharma, A. Cheng, A. Leung, Y. Liu, W. M. Shih, H. Yan, J. Am. Chem. Soc. 2009, 131, 15903-15908.
40. R. Chhabra, J. Sharma, Y. Ke, Y. Liu, S. Rinker, S. Lindsay, H. Yan, J. Am. Chem. Soc. 2007, 129, 10304-10305
41. W. Shen, H. Zhong, D. Neff, M. L. Norton, J. Am. Chem. Soc. 2009, 131, 6660-6661
42. A. Kuzyk, K. T. Laitinen, P. Torma, Nanotechnology 2009, 20, 235305-235310
43. A. Kuzuya, M. Kimura, K. Numajiri, N. Koshi, T. Ohnishi, F. Okada, M. Komiyama, ChemBioChem 2009, 10, 1811-1815
44. K. Numajiri, M. Kimura, A. Kuzuya, M. Komiyama, Chem. Commun. 2010, 46, 5127-5129.
45. S. Pal, Z. Deng, B. Ding, H. Yan, Y. Liu, Angew. Chem. 2010, 122, 2760-2764
46. Angew. Chem. Int. Ed. 2010, 49, 2700-2704
47. B. Ding, Z. Deng, H. Yan, S. Cabrini, R. N. Zuckermann, J. Bokor, J. Am. Chem. Soc. 2010, 132, 3248-3249.
48. N. Stephanopoulos, M. Liu, G. J. Tong, Z. Li, Y. Liu, H. Yan, M. B. Francis, Nano Lett. 2010, 10, 2714-2720
49. H. T. Maune, S.-P. Han, R. D. Barish, M. Bockrath, W. A. Goddard III, P. W. K. Rothemund, E. Winfree, Nat. Nanotechnol. 2010, 5, 61-66.
50. S. M. Douglas, J. J. Chou, W. M. Shih, Proc. Natl. Acad. Sci. USA 2007, 104, 6644-6648.
51. Y. Ke, S. Lindsay, Y. Chang, Y. Liu, H. Yan, Science 2008, 319, 180-183.
52. N. V. Voigt, T. Torring, A. Rotaru, M. F. Jacobsen, J. B. Ravnsbaek, R. Subramani, W. Mamdouh, J. Kjems, A. Mokhir, F. Besenbacher, K. V. Gothelf, Nat. Nanotechnol. 2010, 5, 200-203.
53. S. Helmig, A. Rotaru, D. Arian, L. Kovbasyuk, J. Arnbjerg, P. R. Ogilby, J. Kjems, A. Mokhir, F. Besenbacher, K. V. Gothelf, ACS Nano 2010, 4, 7475-7480.
54. M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, Angew. Chem. Int. Ed. 2010, 49, 9412-9416; also reference [12].
55. I. H. Stein, C. Steinhauer, P. Tinnefeld, J. Am. Chem. Soc. 2011, 133, 4193-4195.
56. H. K. K. Subramanian, B. Chakraborty, R. Sha, N. C. Seeman, Nano Lett. 2011, 11, 910-913.
57. Y. Sannohe, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 2010, 132, 16311-16313.
58. C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, P. Tinnefeld, Angew. Chem. 2009, 121, 9030-9034
59. Angew. Chem. Int. Ed. 2009, 48, 8870-8873
60. R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, F. C. Simmel, Nano Lett. 2010, 10, 4756-4761; see also reference [25].
61. U. R. Mueller, D. V. Nicolau, Microarray Technology and its Applications, Springer, Berlin, 2005
62. M. Schena, D. Shalon, R. W. Davis, P. O. Brown, Science 1995, 270, 467-470.
63. S. A. Bustin, T. Nolan, in Real-Time PCR: An Essential Guide (Eds.:, K. Edwards, J. Logan, N. Saunders,), Horizon Bioscience, Norfolk, 2004.
64. C. E. Castro, F. Kilchherr, D.-N. Kim, E. L. Shiao, T. Wauer, P. Wortmann, M. Bathe, H. Dietz, Nat. Methods 2011, 8, 221-229.
65. Q. Mei, X. Wei, F. Su, Y. Liu, C. Youngbull, R. Johnson, S. Lindsay, H. Yan, D. Meldrum, Nano. Lett. 2011, 11, 1477-1482.
66. S. Rinker, Y. Ke, Y. Liu, R. Chhabra, H. Yan, Nat. Nanotechnol. 2008, 3, 418-422.
67. F. S. Collins, M. S. Guyer, A. Chakravarti, Science 1997, 278, 1580-1581
68. A. J. Schafer, J. R. Hawkins, Nat. Biotechnol. 1998, 16, 33-39
69. A-C. Syvanen, Nat. Rev. Genet. 2001, 2, 930-942
70. E. Lai, Genome Res. 2001, 11, 927-929.
71. U. Landegren, M. Nilsson, P-Y. Kwok, Genome Res. 1998, 8, 769-776
72. A. Rajendran, V. Thiagarajan, B. Rajendar, S. Nishizawa, N. Teramae, Biochim. Biophys. Acta Gen. Subj. 2009, 1790, 95-100
73. A. Rajendran, C. Zhao, B. Rajendar, V. Thiagarajan, Y. Sato, S. Nishizawa, N. Teramae, Biochim. Biophys. Acta Gen. Subj. 2010, 1800, 599-610
74. V. Thiagarajan, A. Rajendran, H. Satake, S. Nishizawa, N. Teramae, ChemBioChem 2010, 11, 94-100
75. B. Rajendar, A. Rajendran, Z. Ye, E. Kanai, Y. Sato, S. Nishizawa, M. Sikorski, N. Teramae, Org. Biomol. Chem. 2010, 8, 4949-4959
76. B. Rajendar, A. Rajendran, Y. Sato, S. Nishizawa, N. Teramae, Bioorg. Med. Chem. 2009, 17, 351-359
77. C. Zhao, A. Rajendran, Q. Dai, S. Nishizawa, N. Teramae, Anal. Sci. 2008, 24, 693-695
78. A. Okamoto, K. Tanaka, T. Fukuta, I. Saito, J. Am. Chem. Soc. 2003, 125, 9296-9297
79. K. Nakatani, S. Sando, I. Saito, Nat. Biotechnol. 2001, 19, 51-55.
80. I. G. Panyutin, P. Hsieh, Proc. Natl. Acad. Sci. USA 1994, 91, 2021-2025
81. S. Q. Wang, X. H. Wang, S. H. Chen, W. Guan, Anal. Biochem. 2002, 309, 206-211.
82. Z. Zhang, Y. Wang, C. Fan, C. Li, Y. Li, L. Qian, Y. Fu, Y. Shi, J. Hu, L. He, Adv. Mater. 2010, 22, 2672-2675.
83. A. Rajendran, S. Nakano, N. Sugimoto, Chem. Commun. 2010, 46, 1299-1301
84. G. Wang, K. M. Vasquez, Mutat. Res. 2006, 598, 103-119.
85. W. E. Wright, V. M. Tesmer, K. E. Huffman, S. D. Levene, J. W. Shay, Genes Dev. 1997, 11, 2801-2809
86. V. L. Makarov, Y. Hirose, J. P. Langmore, Cell 1997, 88, 657-666.
87. J. L. Mergny, C. Helene, Nat. Med. 1998, 4, 1366-1367
88. S. Neidle, G. Parkinson, Nat. Drug Discov. 2002, 1, 383-393
89. L. H. Hurley, Nat. Rev. Cancer 2002, 2, 188-200.
90. T. Mashimo, H. Yagi, Y. Sannohe, A. Rajendran, H. Sugiyama, J. Am. Chem. Soc. 2010, 132, 14910-14918
91. Y. Sannohe, H. Sugiyama, Curr. Protoc. Nucl. Acid Chem. 2010, 40, 17.2.1- 17.2.17; see also references [39] and [40].
92. Z. Yang, J. F. Carey, J. J. Champoux, FEBS J. 2009, 276, 5906-5919
93. S. Shuman, D. G. Bear, J. Sekiguchi, EMBO J. 1997, 16, 6584-6589
94. A. Patel, L. Yakovleva, S. Shuman, A. Mondragon, Structure 2010, 18, 725-733.
95. R. Subramani, S. Juul, A. Rotaru, F. F. Andersen, K. V. Gothelf, W. Mamdouh, F. Besenbacher, M. Dong, B. R. Kundsen, ACS Nano 2010, 4, 5969-5977.
96. C. W. Tornoe, C. Christensen, M. Meldal, J. Org. Chem. 2002, 67, 3057-3064.
97. H. C. Kolb, M. G. Finn, K. B. Sharpless, Angew. Chem. 2001, 113, 2056-2075
98. Angew. Chem. Int. Ed. 2001, 40, 2004-2021.
99. H. Liu, T. Torring, M. Dong, C. B. Rosen, F. Besenbacher, K. V. Gothelf, J. Am. Chem. Soc. 2010, 132, 18054-18056.
100. S. E. Halford, J. F. Marko, Nucleic Acids Res. 2004, 32, 3040-3052.
101. S. W. Hell, Nat. Methods 2009, 6, 24-32.
102. R. B. Best, K. A. Merchant, I. V. Gopich, B. Schuler, A. Bax, W. A. Eaton, Proc. Natl. Acad. Sci. USA 2007, 104, 18964-18969
103. B. Schuler, E. A. Lipman, P. J. Steinbach, M. Kumke, W. A. Eaton, Proc. Natl. Acad. Sci. USA 2005, 102, 2754-2759
104. M. J. Rust, M. Bates, X. Zhuang, Nat. Methods 2006, 3, 793-796
105. T. Heinlein, A. Biebricher, P. Schlueter, C. M. Roth, D.-P. Herten, J. Wolfrum, M. Heilemann, C. Mueller, P. Tinnefeld, M. Sauer, ChemPhysChem 2005, 6, 949-955.
106. I. H. Stein, V. Schuller, P. Bohm, P. Tinnefeld, T. Liedl, ChemPhysChem 2011, 12, 689-695.
107. R. Siegwart, I. R. Nourbakhsh, Introduction to Autonomous Mobile Robots, MIT Press, USA, 2004
108. J.-S. Shin, N. A. Pierce, J. Am. Chem. Soc. 2004, 126, 10834-10835
109. W. B. Sherman, N. C. Seeman, Nano Lett. 2004, 4, 1203-1207.
110. H. Gu, J. Chao, S-J. Xiao, N. C. Seeman, Nature 2010, 465, 202-205.
111. H. Yan, X. Zhang, Z. Shen, N. C. Seeman, Nature 2002, 415, 62-65
112. S. Liao, N. C. Seeman, Science 2004, 306, 2072-2074.
113. K. Lund, A. J. Manzo, N. Dabby, N. Michelotti, A. Johnso, n Buck, J. Nangreave, S. Taylor, R. Pei, M. N. Stojanovic, N. G. Walter, E. Winfree, H. Yan, Nature 2010, 465, 206- 210.
114. S. F. J. Wickham, M. Endo, Y. Katsuda, K. Hidaka, J. Bath, H. Sugiyama, A. J. Turberfield, Nat. Nanotechnol. 2011, 6, 166-169.
115. H. Hess, Science 2006, 312, 860-861.
116. A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 2011, 133, 14488-14491.