Selective biomolecular nanoarrays for parallel single-molecule investigations

Journal of the American Chemical Society

Volumn 133, Issue 20, 2011, Pages 7656-7659

  Palma, Matteo ^a   Abramson, Justin J ^a   Gorodetsky, Alon A ^a   Penzo, Erika ^a   Gonzalez, Ruben L ^a   Sheetz, Michael P ^a   Nuckolls, Colin ^a   Hone, James ^a   Wind, Shalom J ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-MOLECULAR; BIOLOGICAL ACTIVITIES; HIGH-THROUGHPUT; NANO SCALE; NANOARRAYS; NANOPATTERNED SURFACES; NANOSCALE CONTROL; NONSPECIFIC ADSORPTION; PROTEIN-DNA BINDING; REAL TIME; SINGLE MOLECULE LEVEL; SINGLE-MOLECULE; SINGLE-MOLECULE RESOLUTION;

ADSORPTION; MOLECULAR BIOLOGY; NANOSTRUCTURED MATERIALS; NANOTECHNOLOGY; SELF ASSEMBLY;

MOLECULES;

NANOMATERIAL; SELF ASSEMBLED MONOLAYER;

ADSORPTION; ARTICLE; HIGH THROUGHPUT SCREENING; MOLECULE; NANOARRAY; NANOTECHNOLOGY; PROTEIN DNA BINDING;

DNA; MICROSCOPY, FLUORESCENCE; NANOSTRUCTURES;

EID: 79957679378     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja201031g     Document Type: Article

References (43)

1. Stephanopoulos, N.; Solis, E. O. P.; Stephanopoulos, G. AIChE J. 2005, 51, 1858
2. Langer, R.; Tirrell, D. A. Nature 2004, 428, 487
3. Rosi, N. L.; Mirkin, C. A. Chem. Rev. 2005, 105, 1547
4. Torres, A. J.; Wu, M.; Holowka, D.; Baird, B. Annu. Rev. Biophys. 2008, 37, 265
5. Wong, L. S.; Khan, F.; Micklefield, J. Chem. Rev. 2009, 109, 4025
6. Nanobiotechnology; Wiley-VCH: Weinheim, Germany, 2004.
7. Aydin, D.; Schwieder, M.; Louban, I.; Knoppe, S.; Ulmer, J.; Haas, T. L.; Walczak, H.; Spatz, J. P. Small 2009, 5, 1014
8. Niwa, D.; Omichi, K.; Motohashi, N.; Homma, T.; Osaka, T. Chem. Lett. 2004, 33, 176
9. Zhang, G. J.; Tanii, T.; Zako, T.; Hosaka, T.; Miyake, T.; Kanari, Y.; Funatsu, T. W.; Ohdomari, I. Small 2005, 1, 833
10. Nicolau, D. V.; Demers, L.; Ginger, D. S. In Microarray Technology and Its Applications; Nicolau, D. V.; Müller, U. R., Eds.; Springer: Berlin, 2005; pp 89-118.
11. Nanobiotechnology II; Wiley-VCH: Weinheim, Germany, 2007.
12. Bulyk, M. L.; Gentalen, E.; Lockhart, D. J.; Church, G. M. Nat. Biotechnol. 1999, 17, 573
13. Demers, L. M.; Ginger, D. S.; Park, S. J.; Li, Z.; Chung, S. W.; Mirkin, C. A. Science 2002, 296, 1836
14. Bruckbauer, A.; Ying, L. M.; Rothery, A. M.; Zhou, D. J.; Shevchuk, A. I.; Abell, C.; Korchev, Y. E.; Klenerman, D. J. Am. Chem. Soc. 2002, 124, 8810
15. Rodolfa, K. T.; Bruckbauer, A.; Zhou, D. J.; Korchev, Y. E.; Klenerman, D. Angew. Chem., Int. Ed. 2005, 44, 6854
16. Huang, S. X.; Schopf, E.; Chen, Y. Nano Lett. 2007, 7, 3116
17. Akbulut, O.; Jung, J. M.; Bennett, R. D.; Hu, Y.; Jung, H. T.; Cohen, R. E.; Mayes, A. M.; Stellacci, F. Nano Lett. 2007, 7, 3493
18. Drmanac, R. Science 2010, 327, 78
19. Ishijima, A.; Yanagida, T. Trends Biochem. Sci. 2001, 26, 438
20. Ritort, F. J. Phys.: Condens. Matter 2006, 18, R531
21. Smiley, R. D.; Hammes, G. G. Chem. Rev. 2006, 106, 3080
22. Houseman, B. T.; Mrkisch, M. Angew. Chem., Int. Ed. 1999, 38, 782
23. Castronovo, M.; Radovic, S.; Grunwald, C.; Casalis, L.; Morgante, M.; Scoles, G. Nano Lett. 2008, 8, 4140
24. Bulyk, M. L. Adv. Biochem. Eng. Biotechnol. 2007, 104, 65
25. Field, S.; Udalova, I.; Ragoussis, J. Adv. Biochem. Eng. Biotechnol. 2007, 104, 87
26. Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides, G. M. Chem. Rev. 2005, 105, 1103
27. Cherniavskaya, O.; Chen, C. J.; Heller, E.; Sun, E.; Provezano, J.; Kam, L.; Hone, J.; Sheetz, M. P.; Wind, S. J. J. Vac. Sci. Technol., B 2005, 23, 2972
28. Avidin-Biotin Technology; Wilchek, M.; Bayer, E. A., Eds.; Methods in Enzymology, Vol. 184; Academic Press: San Diego, CA, 1990.
29. Ladd, J.; Boozer, C.; Yu, Q. M.; Chen, S. F.; Homola, J.; Jiang, S. Langmuir 2004, 20, 8090
30. Smith, C. L.; Milea, J. S.; Nguyen, G. H. Top. Curr. Chem. 2005, 261, 63
31. Indeed, when the metal thiolation step in the functionalization process was performed after the PEG-silane step, we observed that the biotin-thiols physisorbed on the PEG surrounding the nanodots and functioned as anchoring points for streptavidin and consequently for the DNAs, thus increasing the background fluorescence and preventing the resolution of single nanodots via epifluorescence microscopy imaging.
32. Available from New England Biolabs. See: http://www.neb.com/nebecomm/ products/productR3151.asp (accessed Feb 1, 2011).
33. Athanasiadis, A.; Vlassi, M.; Kotsifaki, D.; Tucker, P. A.; Wilson, K. S.; Kokkinidis, M. Nat. Struct. Biol. 1994, 1, 469
34. Photobleaching occurred at a rate that was more than 1 order of magnitude lower than the rate of PvuII cleavage (Figure SI-5). This allowed us confidently to dismiss photobleaching in our single-molecule enzyme data.
35. Lu, H. P.; Xun, L. Y.; Xie, X. S. Science 1998, 282, 1877
36. Xie, S. N. Single Mol. 2001, 2, 229
37. Xie, F. Q.; Dupureur, C. M. Arch. Biochem. Biophys. 2009, 483, 1
38. Xie, F. Q.; Qureshi, S. H.; Papadakos, G. A.; Dupureur, C. M. Biochemistry 2008, 47, 12540
39. Simoncsits, A.; Tjornhammar, M. L.; Rasko, T.; Kiss, A.; Pongor, S. J. Mol. Biol. 2001, 309, 89
40. This was done by counting the number of discrete steplike drops in the fluorescence intensity versus time for trajectories arising from both PvuII activity (on PvuII-treated nanoarrays) and photobleaching (on untreated nanoarrays).
41. The remaining ∼15% of the nanodots lacked discrete steplike drops in fluorescence intensity and instead exhibited a relatively continuous decay likely arising from a large density of immobilized DNAs, thus preventing single-molecule resolution.
42. Jackson, A. M.; Myerson, J. W.; Stellacci, F. Nat. Mater. 2004, 3, 330
43. Schvartzman, M.; Wind, S. J. Nano Lett. 2009, 9, 3629