Distance-dependent emission from dye-labeled oligonucleotides on striped Au/Ag nanowires: Effect of secondary structure and hybridization efficiency

Journal of the American Chemical Society

Volumn 128, Issue 40, 2006, Pages 13243-13254

  Stoermer, Rebecca L ^a   Keating, Christine D ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENCE PATTERNING; HYBRIDIZATION; OLIGONUCLEOTIDES; SURFACE DEFECTS;

CHROMOPHORES; DNA; ELECTROMAGNETIC WAVE EMISSION; FLUORESCENCE; NUCLEIC ACIDS; OLIGOMERS; QUENCHING;

NANOSTRUCTURED MATERIALS;

COMPLEMENTARY DNA; DOUBLE STRANDED DNA; FLUORESCENT DYE; MERCURY; METAL; NUCLEIC ACID; OLIGONUCLEOTIDE; SILVER;

ARTICLE; ELECTROMAGNETIC FIELD; EXPOSURE; FLUORESCENCE; HYBRIDIZATION; OLIGONUCLEOTIDE PROBE; SEPARATION TECHNIQUE; SURFACE PROPERTY;

DNA; DNA PROBES; FLUORESCENT DYES; GOLD; NANOWIRES; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; RHODAMINES; SILVER;

EID: 33749531749     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0637200     Document Type: Article

References (77)

1. Moskovits, M. Rev. Mod. Phys. 1985, 57, 783-826.
2. Chance, R. R.; Prock, A.; Silbey, R. Adv. Chem. Phys. 1978, 37, 1-65.
3. (a) Lakowicz, J. R. Anal. Biochem. 2001, 298, 1-24.
4. (b) Lakowicz, J. R. Anal Biochem. 2005, 337, 171-194.
5. Meitiu, H. Prog. Surf. Sci. 1984, 17, 153-320.
6. Neumann, T.; Johansson, M.-L.; Kambhampati, D.; Knoll, W. Adv. Funct. Mater. 2002, 12, 575-586.
7. Weitz, D. A.; Garoff, S.; Gersten, J. I.; Nitzan, A. J. Chem. Phys. 1983, 78, 5324-5338.
8. Corni, S.; Tomasi, J. J. Chem. Phys. 2003, 118, 6481-6494.
9. (a) Sokolov, K.; Chumanov, G.; Cotton, T. M. Anal. Chem. 1998, 70, 3898-3905.
10. (b) Chumanov, G.; Sokolov, K.; Gregory, B. W.; Cotton, T. M. J. J. Phys. Chem. 1995, 99, 9466-9471.
11. Whitmore, P. M.; Robata, H. J.; Harris, C. B. J. Phys. Chem. 1982, 77, 1560-1568.
12. Yokota, H.; Saito, K.; Yanagida, T. Phys. Rev. Lett. 1998, 80, 4606-4609.
13. Knobloch, H.; Brunner, H.; Leitner. A.; Aussenegg, F.; Knoll, W. J. Phys. Chem. 1993, 98, 10093-10095.
14. (a) Huang, X.; Lee, K. T.; George, T. F. J. Phys. Chem. 1986, 85, 567-572.
15. (b) Glass, A. M.; Liao, P. F.; Bergman, J. G.; Olson, D. H. Opt. Lett. 1980, 5, 368-370.
16. (c) Wokaun, A.; Lutz, H. P.; King, A. P.; Wild, U. P.; Ernst, R. R. J. Phys. Chem. 1983, 79, 509-514.
17. (d) Amos, R. M.; Barnes, W. L. Phys. Rev. B 1999, 59, 7708-7714.
18. (e) Alivisatos, A. P.; Waldeck, D. H.; Harris, C. B. J. Chem. Phys. 1985, 82, 541-547.
19. (f) Zhang, J.; Malicka, J.; Gryczynski, I.; Lakowicz, J. R. J. Chem. Phys. B. 2005, 109, 7643-7648.
20. Aslan, K.; Lakowicz, J. R.; Geddes, C. D. Anal. Bioanal. Chem. 2005, 382, 926-933.
21. Kummerlen, J.; Leitner, A.; Brunner, H.; Aussenegg, F. R.; Wokaun, A. Mol. Phys. 1993, 80, 1031-1046.
22. Tarcha, P. J.; DeSaja-Gonzalez, J.; Rodriguez-Llorente, S.; Aroca, R. Appl. Spectrosc. 1999, 53, 43-48.
23. Schneider, G.; Decher, G.; Nerambourg, N.; Praho, R.; Werts, M. H. V.; Blanchard-Desce, M. Nano Lett. 2006, 6, 530-536.
24. Tovmachenko, O. G.; Graf, C.; van den Heuvel, D. J.; van Blaaderen, A.; Gerritsen, H. C. Adv. Mater. 2006, 18, 91-95.
25. Hong, B.; Kang, K. A. Biosens. Bioelectron. 2006, 21, 1333-1338.
26. Stranik, O.; McEvoy, H. M.; McDonagh, C.; MacCraith, B. D. Sens. Actuators. B 2005, 107, 148-153.
27. Zhang, J.; Lakowicz, J. R. J. Phys. Chem. B 2006, 110, 2387-2392.
28. Liebermann, T.; Knoll, W.; Sluka, P.; Herrmann, R. Colloids Surf., A 2000, 169, 337-350.
29. Perez-Luna, V. H.; Yang, S.; Rabinovich, E. M.; Buranda, T.; Sklar, L. A.; Hampton, P. D.; Lopez, G. P. Biosens. Bioelectron. 2002, 17, 71-78.
30. Maxwell, D. J.; Taylor, J. R.; Nie, S. J. Am. Chem. Soc. 2002, 124, 9606-9612.
31. Tyagi, S.; Kramer, F. R. Nat. Biotechnol 1996, 14, 303-308.
32. Heyduk, T.; Heyduk, E. Nat. Biotechnol. 2002, 20, 171-175.
33. Fang, X.; Li, J. J.; Tan, W. Anal. Chem. 2002, 72, 3280-3285.
34. Alberts, D. P.; Parman, J. M.; Goddard, N. L. Biophys. J. 2003, 84, 3212-3217.
35. Antony, T.; Thomas, T.; Sigal, L. H.; Shirahata, A.; Thomas, T. J. Biochemistry 2001, 40, 9387-9395.
36. Bonnet, G.; Tyagi, S.; Libchaber, A.; Kramer, F. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6171-6176.
37. Dubertret, B.; Calame, M.; Libchaber, A. J. Nat. Biotechnol. 2001, 19, 365-370.
38. (a) Fang, X.; Liu, X.; Schuster, S.; Tan, W. J. Am. Chem. Soc. 1999, 121, 2921-2922.
39. (b) Brown, L.; Cummins, J.; Hamilton, A.; Brown, T. Chem. Commun. 2000, 621-622.
40. Liu, X.; Tan, W. Anal. Chem. 1999, 71, 5054-5059.
41. (b) Liu, X.; Farmerie, W.; Schuster, S.; Tan, W. Anal. Biochem. 2000, 283, 56-63.
42. (c) Yao, G.; Tan, W. Anal. Biochem. 2004, 331, 216-223.
43. Steemers, F.; Ferguson, J. A.; Walt, D. R. Nat. Biotechnol. 2000, 18, 91-94.
44. (b) Epstein, J. R.; Leung, A. P. K.; Lee, K.-H.; Walt, D. R. Biosens. Bioelectron. 2003, 18, 541-546.
45. Rang, H.; Li, J.; Liu, H.; Liu, Q.; Mei, Q.; Wang, Y.; Zhu, J.; He, N.; Lu, Z. Nucleic Acids Res. 2002, 30, e61.
46. Du, H.; Strohsahl, C. M.; Camera, J.; Miller, B. L.; Krauss, T. D. J. Am. Chem. Soc. 2005, 127, 7932-7940.
47. Du, H.; Disney, M. D.; Miller, B. L.; Krauss, T. D. J. Am. Chem. Soc. 2003, 125, 4012-4013.
48. Sha, M. Y.; Yamanaka, M.; Walton, I. D.; Norton, S. M.; Stoermer, R. L.; Keating, C. D.; Natan, M. J.; Penn, S. G. Nano Biotechnology 2005, 1, 327-335.
49. Nicewarner-Pena, S. R.; Carado, A. J.; Shale, K. E.; Keating C. D. J. Phys. Chem. B 2003, 107, 7360.
50. Nicewarner-Pena, S. R.; Freeman, R. G.; Reiss, B. D.; He, L.; Pena, D. J.; Walton, I. D.; Cromer, R.; Keating, C. D.; Natan, M. J. Science 2001, 294, 137-141.
51. Keating, C. D.; Natan, M. J. Adv. Mater. 2003, 15, 451-454.
52. Lakowicz, J. R.; Shen, B.; Gryczynski, Z.; D' Auria, S.; Gryczynski, I. Biochem. Biophys. Res. Commun. 2001, 286, 875-879.
53. Malicka, J.; Gryczynski, I.; Fang, J.; Kusba, J.; Lakowicz, J. R. J. Fluorescence 2002, 12, 439-447.
54. Malicka, J.; Gryczynski, I.; Fang, J.; Kusba, J.; Lakowicz, J. R. Anal. Biochem. 2003, 315, 160-169.
55. Malicka, J.; Gryczynski, I.; Maliwal, B. P.; Fang, J.; Lakowicz, J. R. Biopolymers (Biospectroscopy) 2003, 72, 96-104.
56. Malicka, J.; Gryczynski, I.; Lakowicz, J. R. Biochem. Biophys. Res. Commun. 2003, 306, 213-218.
57. Malicka, J.; Gryczynski, I.; Gryczynski, Z.; Lakowicz, J. R. Anal. Chem. 2003, 75, 6629-6633.
58. Malicka, J.; Gryczynski, Z.; Lakowicz, J. R. Anal. Biochem. 2003, 315, 57-66.
59. Rant, U.; Arinaga, K.; Fujita, S.; Yokoyama, N.; Abstreiter, G.; Tornow, M. Langmuir 2004, 20, 10086-10092.
60. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I., Jr. Nucleic Acids: Structures, Properties, and Functions; University Science Books: Sausalito, CA, 2000.
61. Walton, I. D.; Norton, S. M.; Balasingham, A.; He, L.; Oviso, D. F., Jr.; Gupta, D.; RaJu, P. A.; Natan, M. J.; Freeman, R. G. Anal. Chem. 2002, 74, 2240-2247.
62. Zhou, X.-H.; Gao, S. Stat. Med. 1997, 16, 783-790.
63. Demers, L. M.; Mirkin, C. A.; Mucic, R. C.; Reynolds, R. A., III; Leisinger, R. L.; Elghanian, R.; Viswanadham, G. Anal. Chem. 2000, 72, 5535-5541.
64. Wehry, E. L. Molecular Fluorescence and Phosphorescence Spectrometry. In Instrumental Techniques for analytical chemistry; Settle, F. A., Ed.; Prentice Hall: Upper Saddle River, NJ, 1997; pp 507-539.
65. (a) Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. Science 1996, 382, 607-609.
66. (b) Jin, R.; Wu, G.; Li, Z.; Mirkin, C. A.; Schatz, G. C. J. Am. Chem. Soc. 2003, 125, 1653-1654.
67. (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916-8920.
68. (b) Steel, A. B.; Levicky, T. M.; Herne, T. M.; Tarlov, M. J. Biophys. J. 2000, 79, 975-981.
69. (a) Shchepinov, M. S.; Case-Green, S. C.; Southern, E. M. Nucleic Acids Res. 1997, 25, 1155-1161.
70. (b) Southern, E.; Mir, K.; Shchepinov, M. Nat. Genet. 1999, 21, 5-9.
71. Nicewarner-Peña, S. R.; Raina, S.; Goodrich, G. P.; Fedoroff, N. V.; Keating, C.D. J. Am. Chem. Soc. 2002, 124, 7314-7323.
72. Harris, D. C. Quantitative Chemical Analysis, 4th ed.; W. H. Freeman and Company: New York, 1995.
73. Herrwerth, S.; Eck, W.; Reinhardt, S.; Grunze, M. J. Am. Chem. Soc. 2003, 125, 9359-9366.
74. Ulman, A. Chem. Rev. 1996, 96, 1533-1554.
75. Stoermer, R. L.; Sioss, J. A.; Keating, C. D. Chem. Mater. 2005, 17, 4356-4361.
76. Maliwal, B. P.; Malicka, J.; Gryczynski, I.; Gryczynski, Z.; Lakowicz, J. R. Biopolymers (Biospectroscopy) 2003, 70, 585-594.
77. www.idtdna.com, accessed May 27, 2006.