Fluorescent silver nanoclusters as DNA probes

Nanoscale

Volumn 5, Issue 18, 2013, Pages 8443-8461

  Obliosca, Judy M ^a   Liu, Cong ^a   Yeh, Hsin Chih ^a  

^a The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA PROBE; DNA SENSING; ENVIRONMENTAL SENSITIVITIES; NEW FLUORESCENT PROBES; SILVER NANOCLUSTERS; SPECIFIC DETECTION;

DNA; FLUORESCENCE; NANOCLUSTERS;

SILVER;

DNA; DNA PROBE; METAL NANOPARTICLE; SILVER;

CHEMISTRY; DNA PROBE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; NUCLEIC ACID HYBRIDIZATION; SINGLE NUCLEOTIDE POLYMORPHISM; REVIEW;

DNA; DNA PROBES; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; METAL NANOPARTICLES; NUCLEIC ACID HYBRIDIZATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SILVER;

EID: 84881604835     PISSN: 20403364     EISSN: 20403372     Source Type: Journal    
DOI: 10.1039/c3nr01601c     Document Type: Article

References (205)

1. H. Kobayashi M. Ogawa R. Alford P. L. Choyke Y. Urano New strategies for fluorescent probe design in medical diagnostic imaging Chem. Rev. 2010 110 2620
2. J. Zheng R. M. Dickson Individual water-soluble dendrimer-encapsulated silver nanodot fluorescence J. Am. Chem. Soc. 2002 124 13982
3. J. Zheng C. Zhang R. M. Dickson Highly fluorescent, water-soluble, size-tunable gold quantum dots Phys. Rev. Lett. 2004 93 077402
4. J. T. Petty J. Zheng N. V. Hud R. M. Dickson DNA-templated Ag nanocluster formation J. Am. Chem. Soc. 2004 126 5207
5. C. M. Ritchie K. R. Johnsen J. R. Kiser Y. Antoku R. M. Dickson J. T. Petty Ag nanocluster formation using a cytosine oligonucleotide template J. Phys. Chem. C 2007 111 175
6. T. Vosch Y. Antoku J.-C. Hsiang C. I. Richards J. I. Gonzalez R. M. Dickson Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores Proc. Natl. Acad. Sci. U. S. A. 2007 104 12616
7. E. G. Gwinn P. O'Neill A. J. Guerrero D. Bouwmeester D. K. Fygenson Sequence-dependent fluorescence of DNA-hosted silver nanoclusters Adv. Mater. 2008 20 279
8. C. I. Richards S. Choi J.-C. Hsiang Y. Antoku T. Vosch A. Bongiorno Y.-L. Tzeng R. M. Dickson Oligonucleotide-stabilized Ag nanocluster fluorophores J. Am. Chem. Soc. 2008 130 5038
9. C. I. Richards J.-C. Hsiang D. Senapati S. A. Patel J. Yu T. Vosch R. M. Dickson Optically modulated fluorophores for selective fluorescence signal recovery J. Am. Chem. Soc. 2009 131 4619
10. J. Sharma H.-C. Yeh H. Yoo J. H. Werner J. S. Martinez A complementary palette of fluorescent silver nanoclusters Chem. Commun. 2010 46 3280
11. H.-C. Yeh J. Sharma J. J. Han J. S. Martinez J. H. Werner A DNA-silver nanocluster probe that fluoresces upon hybridization Nano Lett. 2010 10 3106
12. H.-C. Yeh J. Sharma H. Yoo J. S. Martinez J. H. Werner Photophysical characterization of fluorescent metal nanoclusters synthesized using oligonucleotides, proteins and small molecule ligands Proc. SPIE-Int. Soc. Opt. Eng. 2010 7576 75760N
13. H.-C. Yeh J. Sharma J. J. Han J. S. Martinez J. H. Werner A beacon of light - a new molecular probe for homogeneous detection of nucleic acid targets IEEE Nanotechnol. Mag. 2011 5 28
14. M. L. Neidig J. Sharma H.-C. Yeh J. S. Martinez S. D. Conradson A. P. Shreve Ag K-edge EXAFS analysis of DNA-templated fluorescent silver nanoclusters: insight into the structural origins of emission tuning by DNA sequence variations J. Am. Chem. Soc. 2011 133 11837
15. J. Sharma H.-C. Yeh H. Yoo J. H. Werner J. S. Martinez Silver nanocluster aptamers: in situ generation of intrinsically fluorescent recognition ligands for protein detection Chem. Commun. 2011 47 2294
16. P. R. O'Neill E. G. Gwinn D. K. Fygenson UV excitation of DNA stabilized Ag cluster fluorescence via the DNA bases J. Phys. Chem. C 2011 115 24061
17. H.-C. Yeh J. Sharma I. M. Shih D. M. Vu J. S. Martinez J. H. Werner A fluorescence light-up Ag nanocluster probe that discriminates single-nucleotide variants by emission color J. Am. Chem. Soc. 2012 134 11550
18. J. Sharma R. C. Rocha M. L. Phipps H.-C. Yeh K. A. Balatsky D. M. Vu A. P. Shreve J. H. Werner J. S. Martinez A DNA-templated fluorescent silver nanocluster with enhanced stability Nanoscale 2012 4 4107
19. S. H. Yau N. Abeyasinghe M. Orr L. Upton O. Varnavski J. H. Werner H.-C. Yeh J. Sharma A. P. Shreve J. S. Martinez T. Goodson III Bright two-photon emission and ultra-fast relaxation dynamics in a DNA-templated nanocluster investigated by ultra-fast spectroscopy Nanoscale 2012 4 4247
20. J. Yu S. Choi R. M. Dickson Shuttle-based fluorogenic silver-cluster biolabels Angew. Chem., Int. Ed. 2009 48 318
21. S. Choi J. Yu S. A. Patel Y.-L. Tzeng R. M. Dickson Tailoring silver nanodots for intracellular staining Photochem. Photobiol. Sci. 2011 10 109
22. J. T. Petty S. P. Story J.-C. Hsiang R. M. Dickson DNA-templated molecular silver fluorophores J. Phys. Chem. Lett. 2013 4 1148 1155
23. S. Choi R. M. Dickson J. Yu Developing luminescent silver nanodots for biological applications Chem. Soc. Rev. 2012 41 1867
24. I. Díez R. H. Ras Fluorescent silver nanoclusters Nanoscale 2011 3 1963
25. H. X. Xu K. S. Suslick Water-soluble fluorescent silver nanoclusters Adv. Mater. 2010 22 1078
26. L. Shang S. Dong G. U. Nienhaus Ultra-small fluorescent metal nanoclusters: synthesis and biological applications Nano Today 2011 6 401
27. S. J. Guo E. K. Wang Noble metal nanomaterials: controllable synthesis and application in fuel cells and analytical sensors Nano Today 2011 6 240
28. B. Han E. Wang DNA-templated fluorescent silver nanoclusters Anal. Bioanal. Chem. 2012 402 129
29. A. Latorre A. Somoza DNA-mediated silver nanoclusters: synthesis, properties and applications ChemBioChem 2012 13 951
30. J. T. Petty C. Fan S. P. Story B. Sengupta M. Sartin J.-C. Hsiang J. W. Perry R. M. Dickson Optically enhanced, near-IR, silver cluster emission altered by single base changes in the DNA template J. Phys. Chem. B 2011 115 7996
31. J. Zheng P. R. Nicovich R. M. Dickson Highly fluorescent noble-metal quantum dots Annu. Rev. Phys. Chem. 2007 58 409
32. R. Jin Quantum sized, thiolate-protected gold nanoclusters Nanoscale 2010 2 343
33. A. Henglein P. Mulvaney T. Linnert Chemistry of Agn aggregates in aqueous solution: non-metallic oligomeric clusters and metallic particles Faraday Discuss. 1991 92 31
34. S. Patel, Photophysics of fluorescent silver nanoclusters, PhD Dissertation, Georgia Institute of Technology, 2009, p. 1
35. G. Schmid Large clusters and colloids. Metals in the embryonic state Chem. Rev. 1992 92 1709
36. C. M. Aikens Electronic structure of ligand-passivated gold and silver nanoclusters J. Phys. Chem. Lett. 2011 2 99
37. L. Brewer B. King J. Wang B. Meyer G. Moore Absorption spectrum of silver atoms in solid argon, krypton, and xenon J. Chem. Phys. 1968 49 5209
38. 4 in an argon matrix Chem. Phys. Lett. 1999 313 105
39. 3 clusters Chem. Phys. Lett. 2000 320 59
40. 3 species in the course of condensation of Ag atoms with Ar ChemPhysChem 2004 5 403
41. P. Radcliffe A. Przystawik T. Diederich T. Döppner J. Tiggesbäumker K.-H. Meiwes-Broer Excited-state relaxation of Ag-{8} clusters embedded in helium droplets Phys. Rev. Lett. 2004 92 173403
42. W. Lesniak A. U. Bielinska K. Sun K. W. Janczak X. Shi J. R. Baker, Jr L. P. Balogh Silver/dendrimer nanocomposites as biomarkers: fabrication, characterization, in vitro toxicity, and intracellular detection Nano Lett. 2005 5 2123
43. L. Shang S. J. Dong Facile preparation of water-soluble fluorescent silver nanoclusters using a polyelectrolyte template Chem. Commun. 2008 1088
44. B. G. Ershov A. Henglein Reduction of Ag+ on polyacrylate chains in aqueous solution J. Phys. Chem. B 1998 102 10663
45. Z. Shen H. W. Duan H. Frey Water-soluble fluorescent Ag nanoclusters obtained from multiarm star poly(acrylic acid) as "molecular hydrogel" templates Adv. Mater. 2007 19 349
46. J. G. Zhang S. Q. Xu E. Kumacheva Photogeneration of fluorescent silver nanoclusters in polymer microgels Adv. Mater. 2005 17 2336
47. S. Pal R. Varghese Z. T. Deng Z. Zhao A. Kumar H. Yan Y. Liu Site-specific synthesis and in situ immobilization of fluorescent silver nanoclusters on DNA nanoscaffolds by use of the tollens reaction Angew. Chem., Int. Ed. 2011 50 4176
48. T. Udaya Bhaskara Rao T. Pradeep Luminescent Ag7 and Ag8 clusters by interfacial synthesis Angew. Chem., Int. Ed. 2010 49 3925
49. B. Adhikari A. Banerjee Facile synthesis of water-soluble fluorescent silver nanoclusters and HgII sensing Chem. Mater. 2010 22 4364
50. N. Cathcart P. Mistry C. Makra B. Pietrobon N. Coombs M. Jelokhani-Niaraki V. Kitaev Chiral thiol-stabilized silver nanoclusters with well-resolved optical transitions synthesized by a facile etching procedure in aqueous solutions Langmuir 2009 25 5840
51. J. Yu S. A. Patel R. M. Dickson In vitro and intracellular production of peptide-encapsulated fluorescent silver nanoclusters Angew. Chem., Int. Ed. 2007 46 2028
52. Y. Antoku J.-I. Hotta H. Mizuno R. M. Dickson J. Hofkens T. Vosch Transfection of living HeLa cells with fluorescent poly-cytosine encapsulated Ag nanoclusters Photochem. Photobiol. Sci. 2010 9 716
53. X. Le Guével C. Spies N. Daum G. Jung M. Schneider Highly fluorescent silver nanoclusters stabilized by glutathione: a promising fluorescent label for bioimaging Nano Res. 2012 5 379
54. D. Schultz K. Gardner S. S. Oemrawsingh N. MarkeŠević K. Olsson M. Debord D. Bouwmeester E. Gwinn Evidence for rod-shaped DNA-stabilized silver nanocluster emitters Adv. Mater. 2013 25 2797
55. S. A. Patel C. I. Richards J.-C. Hsiang R. M. Dickson Water-soluble Ag nanoclusters exhibit strong two-photon-induced fluorescence J. Am. Chem. Soc. 2008 130 11602
56. C. Xu W. W. Webb Measurement of two-photon excitation cross-sections of molecular fluorophores with data from 690 to 1050 nm J. Opt. Soc. Am. B 1996 13 481
57. P. R. O'Neill L. R. Velazquez D. G. Dunn E. G. Gwinn D. K. Fygenson Hairpins with poly-C loops stabilize four types of fluorescent Ag-n: DNA J. Phys. Chem. C 2009 113 4229
58. P. R. O'Neill K. Young D. Schiffels D. K. Fygenson Few-atom fluorescent silver clusters assemble at programmed sites on DNA nanotubes Nano Lett. 2012 12 5464
59. D. Schultz E. Gwinn Stabilization of fluorescent silver clusters by RNA homopolymers and their DNA analogs: C, G versus A, T (U) dichotomy Chem. Commun. 2011 47 4715
60. J. H. Yu S. M. Choi C. I. Richards Y. Antoku R. M. Dickson Live cell surface labeling with fluorescent Ag nanocluster conjugates Photochem. Photobiol. 2008 84 1435
61. T. Li L. B. Zhang J. Ai S. J. Dong E. K. Wang Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device ACS Nano 2011 5 6334
62. W. Guo J. Yuan E. Wang Oligonucleotide-stabilized Ag nanoclusters as novel fluorescence probes for the highly selective and sensitive detection of the Hg2+ ion Chem. Commun. 2009 3395
63. G. Y. Lan C. C. Huang H. T. Chang Silver nanoclusters as fluorescent probes for selective and sensitive detection of copper ions Chem. Commun. 2010 46 1257
64. J. Li X. Zhong H. Zhang X. C. Le J. J. Zhu Binding-induced fluorescence turn-on assay using aptamer-functionalized silver nanocluster DNA probes Anal. Chem. 2012 84 5170
65. J. J. Liu X. R. Song Y. W. Wang A. X. Zheng G. N. Chen H. H. Yang Label-free and fluorescence turn-on aptasensor for protein detection via target-induced silver nanoclusters formation Anal. Chim. Acta 2012 749 70
66. S. Tyagi F. R. Kramer Molecular beacons: probes that fluoresce upon hybridization Nat. Biotechnol. 1996 14 303
67. A. Miyawaki J. Llopis R. Heim J. M. McCaffery J. A. Adams M. Ikura R. Y. Tsien Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin Nature 1997 388 882
68. A. Y. Ting K. H. Kain R. L. Klemke R. Y. Tsien Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells Proc. Natl. Acad. Sci. U. S. A. 2001 98 15003
69. J. Zhang Y. L. Ma S. S. Taylor R. Y. Tsien Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering Proc. Natl. Acad. Sci. U. S. A. 2001 98 14997
70. I. L. Medintz A. R. Clapp H. Mattoussi E. R. Goldman B. Fisher J. M. Mauro Self-assembled nanoscale biosensors based on quantum dot FRET donors Nat. Mater. 2003 2 630
71. A. N. Glazer H. S. Rye Stable dye-DNA intercalation complexes as reagents for high-sensitivity fluorescence detection Nature 1992 359 859
72. N. Svanvik G. Westman D. Y. Wang M. Kubista Light-up probes: thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution Anal. Biochem. 2000 281 26
73. L. H. Chen D. W. McBranch H. L. Wang R. Helgeson F. Wudl D. G. Whitten Highly sensitive biological and chemical sensors based on reversible fluorescence quenching in a conjugated polymer Proc. Natl. Acad. Sci. U. S. A. 1999 96 12287
74. J. P. Knemeyer N. Marme M. Sauer Probes for detection of specific DNA sequences at the single-molecule level Anal. Chem. 2000 72 3717
75. J. Zhang R. E. Campbell A. Y. Ting R. Y. Tsien Creating new fluorescent probes for cell biology Nat. Rev. Mol. Cell Biol. 2002 3 906
76. S. Cabantous T. C. Terwilliger G. S. Waldo Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein Nat. Biotechnol. 2005 23 102
77. T. Ozawa Y. Natori M. Sato Y. Umezawa Imaging dynamics of endogenous mitochondrial RNA in single living cells Nat. Methods 2007 4 413
78. M. Valencia-Burton R. M. McCullough C. R. Cantor N. E. Broude RNA visualization in live bacterial cells using fluorescent protein complementation Nat. Methods 2007 4 421
79. B. A. Griffin S. R. Adams R. Y. Tsien Specific covalent labeling of recombinant protein molecules inside live cells Science 1998 281 269
80. S. R. Adams R. E. Campbell L. A. Gross B. R. Martin G. K. Walkup Y. Yao J. Llopis R. Y. Tsien New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications J. Am. Chem. Soc. 2002 124 6063
81. J. R. Babendure S. R. Adams R. Y. Tsien Aptamers switch on fluorescence of triphenylmethane dyes J. Am. Chem. Soc. 2003 125 14716
82. C. Szent-Gyorgyi B. A. Schmidt Y. Creeger G. W. Fisher K. L. Zakel S. Adler J. A. J. Fitzpatrick C. A. Woolford Q. Yan K. V. Vasilev P. B. Berget M. P. Bruchez J. W. Jarvik A. Waggoner Fluorogen-activating single-chain antibodies for imaging cell surface proteins Nat. Biotechnol. 2008 26 235
83. J. S. Paige K. Y. Wu S. R. Jaffrey RNA mimics of green fluorescent protein Science 2011 333 642
84. N. R. Conley A. K. Pomerantz H. Wang R. J. Twieg W. E. Moerner Bulk and single-molecule characterization of an improved molecular beacon utilizing H-dimer excitonic behavior J. Phys. Chem. B 2007 111 7929
85. M. Ogawa N. Kosaka P. L. Choyke H. Kobayashi H-type dimer formation of fluorophores: a mechanism for activatable, in vivo optical molecular imaging ACS Chem. Biol. 2009 4 535
86. Y. Kitamura T. Ihara Y. Tsujimura Y. Osawa M. Tazaki A. Jyo Colorimetric allele typing through cooperative binding of DNA probes carrying a metal chelator for luminescent lanthanide ions Anal. Biochem. 2006 359 259
87. Y. Kitamura T. Ihara Y. Tsujimura Y. Osawa D. Sasahara M. Yamamoto K. Okada M. Tazaki A. Jyo Template-directed formation of luminescent lanthanide complexes: versatile tools for colorimetric identification of single nucleotide polymorphism J. Inorg. Biochem. 2008 102 1921
88. K. Ebata M. Masuko H. Ohtani M. Kashiwasakejibu Nucleic-acid hybridization accompanied with excimer formation from two pyrene-labeled probes Photochem. Photobiol. 1995 62 836
89. M. Masuko H. Ohtani K. Ebata A. Shimadzu Optimization of excimer-forming two-probe nucleic acid hybridization method with pyrene as a fluorophore Nucleic Acids Res. 1998 26 5409
90. P. L. Paris J. M. Langenhan E. T. Kool Probing DNA sequences in solution with a monomer-excimer fluorescence color change Nucleic Acids Res. 1998 26 3789
91. Y. Chen C. J. Yang Y. Wu P. Conlon Y. Kim H. Lin W. Tan Light-switching excimer beacon assays for ribonuclease H kinetic study ChemBioChem 2008 9 355
92. C. J. Yang S. Jockusch M. Vicens N. J. Turro W. H. Tan Light-switching excimer probes for rapid protein monitoring in complex biological fluids Proc. Natl. Acad. Sci. U. S. A. 2005 102 17278
93. D. A. Heller E. S. Jeng T. K. Yeung B. M. Martinez A. E. Moll J. B. Gastala M. S. Strano Optical detection of DNA conformational polymorphism on single-walled carbon nanotubes Science 2006 311 508
94. D. A. Heller H. Jin B. M. Martinez D. Patel B. M. Miller T.-K. Yeung P. V. Jena C. Hobartner T. Ha S. K. Silverman M. S. Strano Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes Nat. Nanotechnol. 2009 4 114
95. D. A. Heller G. W. Pratt J. Zhang N. Nair A. J. Hansborough A. A. Boghossian N. F. Reuel P. W. Barone M. S. Strano Peptide secondary structure modulates single-walled carbon nanotube fluorescence as a chaperone sensor for nitroaromatics Proc. Natl. Acad. Sci. U. S. A. 2011 108 8544
96. T. N. Grossmann O. Seitz DNA-catalyzed transfer of a reporter group J. Am. Chem. Soc. 2006 128 15596
97. T. N. Grossmann O. Seitz Nucleic acid templated reactions: consequences of probe reactivity and readout strategy for amplified signaling and sequence selectivity Chem.-Eur. J. 2009 15 6723
98. J. L. Mergny A. S. Boutorine T. Garestier F. Belloc M. Rougee N. V. Bulychev A. A. Koshkin J. Bourson A. V. Lebedev B. Valeur N. T. Thuong C. Helene Fluorescence energy transfer as a probe for nucleic acid structures and sequences Nucleic Acids Res. 1994 22 920
99. R. A. Cardullo S. Agrawal C. Flores P. C. Zamecnik D. E. Wolf Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer Proc. Natl. Acad. Sci. U. S. A. 1988 85 8790
100. D. M. Kolpashchikov Binary probes for nucleic acid analysis Chem. Rev. 2010 110 4709
101. M. Vendrell D. Zhai J. C. Er Y.-T. Chang Combinatorial strategies in fluorescent probe development Chem. Rev. 2012 112 4391
102. Y. N. Teo E. T. Kool DNA-multichromophore systems Chem. Rev. 2012 112 4221
103. Y. Yang Q. Zhao W. Feng F. Li Luminescent chemodosimeters for bioimaging Chem. Rev. 2012 113 192
104. R. T. Ranasinghe T. Brown Ultrasensitive fluorescence-based methods for nucleic acid detection: towards amplification-free genetic analysis Chem. Commun. 2011 47 3717
105. T. Ihara Y. Kitamura Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications J. Photochem. Photobiol., C 2012 13 148
106. X. Cheng G. Chen W. R. Rodriguez Micro-and nanotechnology for viral detection Anal. Bioanal. Chem. 2009 393 487
107. K. A. Frazer D. G. Ballinger D. R. Cox D. A. Hinds L. L. Stuve R. A. Gibbs J. W. Belmont A. Boudreau P. Hardenbol S. M. Leal A second generation human haplotype map of over 3.1 million SNPs Nature 2007 449 851
108. B. Budowle M. W. Allard M. R. Wilson R. Chakraborty Forensics and mitochondrial DNA: applications, debates, and foundations Annu. Rev. Genomics Hum. Genet. 2003 4 119
109. D. Pinkel R. Segraves D. Sudar S. Clark I. Poole D. Kowbel C. Collins W.-L. Kuo C. Chen Y. Zhai High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays Nat. Genet. 1998 20 207
110. G. Sozzi D. Conte L. Mariani S. L. Vullo L. Roz C. Lombardo M. A. Pierotti L. Tavecchio Analysis of circulating tumor DNA in plasma at diagnosis and during follow-up of lung cancer patients Cancer Res. 2001 61 4675
111. H. C. Fan W. Gu J. Wang Y. J. Blumenfeld Y. Y. El-Sayed S. R. Quake Non-invasive prenatal measurement of the fetal genome Nature 2012 487 320
112. C. A. Heid J. Stevens K. J. Livak P. M. Williams Real time quantitative PCR Genome Res. 1996 6 986
113. T. Hunkapiller R. Kaiser B. Koop L. Hood Large-scale and automated DNA sequence determination Science 1991 254 59
114. O. Brown Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995 270 467
115. A. Raj P. van den Bogaard S. A. Rifkin A. van Oudenaarden S. Tyagi Imaging individual mRNA molecules using multiple singly labeled probes Nat. Methods 2008 5 877
116. S. Tyagi D. P. Bratu F. R. Kramer Multicolor molecular beacons for allele discrimination Nat. Biotechnol. 1998 16 49
117. R. Elghanian J. J. Storhoff R. C. Mucic R. L. Letsinger C. A. Mirkin Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles Science 1997 277 1078
118. K. Sato K. Hosokawa M. Maeda Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization J. Am. Chem. Soc. 2003 125 8102
119. H. Li L. Rothberg Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles Proc. Natl. Acad. Sci. U. S. A. 2004 101 14036
120. W. Guo J. Yuan Q. Dong E. Wang Highly sequence-dependent formation of fluorescent silver nanoclusters in hybridized DNA duplexes for single nucleotide mutation identification J. Am. Chem. Soc. 2010 132 932
121. Y. Antoku, Fluorescent polycytosine-encapsulated silver nanoclusters, PhD Dissertation, Georgia Institute of Technology, 2007, p. 1
122. B. Sengupta C. M. Ritchie J. G. Buckman K. R. Johnsen P. M. Goodwin J. T. Petty Base-directed formation of fluorescent silver clusters J. Phys. Chem. C 2008 112 18776
123. R. L. Affleck W. P. Ambrose J. N. Demas P. M. Goodwin J. A. Schecker J. M. Wu R. A. Keller Reduction of luminescent background in ultrasensitive fluorescence detection by photobleaching Anal. Chem. 1996 68 2270
124. M. Zhang S. M. Guo Y. R. Li P. Zuo B. C. Ye A label-free fluorescent molecular beacon based on DNA-templated silver nanoclusters for detection of adenosine and adenosine deaminase Chem. Commun. 2012 48 5488
125. C. A. M. Seidel A. Schulz M. H. M. Sauer Nucleobase-specific quenching of fluorescent dyes. 1. nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies J. Phys. Chem. 1996 100 5541
126. J. Widengren J. Dapprich R. Rigler Fast interactions between Rh6G and dGTP in water studied by fluorescence correlation spectroscopy Chem. Phys. 1997 216 417
127. M. Sauer K. H. Drexhage U. Lieberwirth R. Muller S. Nord C. Zander Dynamics of the electron transfer reaction between an oxazine dye and DNA oligonucleotides monitored on the single-molecule level Chem. Phys. Lett. 1998 284 153
128. M. Torimura S. Kurata K. Yamada T. Yokomaku Y. Kamagata T. Kanagawa R. Kurane Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base Anal. Sci. 2001 17 155
129. I. Nazarenko R. Pires B. Lowe M. Obaidy A. Rashtchian Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes Nucleic Acids Res. 2002 30 2089
130. H.-C. Yeh C. M. Puleo Y.-P. Ho V. J. Bailey T. C. Lim K. Liu T.-H. Wang Tunable blinking kinetics of Cy5 for precise DNA quantification and single-nucleotide difference detection Biophys. J. 2008 95 729
131. T. Heinlein J.-P. Knemeyer O. Piestert M. H. M. Sauer Photoinduced electron transfer between fluorescent dyes and guanosine residues in DNA-hairpins J. Phys. Chem. B 2003 107 7957
132. G. S. Ginsburg J. J. McCarthy Personalized medicine: revolutionizing drug discovery and patient care Trends Biotechnol. 2001 19 491
133. K. Nakatani Chemistry challenges in SNP typing ChemBioChem 2004 5 1623
134. P. Y. Kwok Methods for genotyping single nucleotide polymorphisms Annu. Rev. Genomics Hum. Genet. 2001 2 235
135. A. C. Syvanen Accessing genetic variation: genotyping single nucleotide polymorphisms Nat. Rev. Genet. 2001 2 930
136. P.-Y. Kwok X. Chen Detection of single nucleotide polymorphisms Curr. Issues Mol. Biol. 2003 5 43
137. J. M. Shumaker A. Metspalu C. T. Caskey Mutation detection by solid phase primer extension Hum. Mutat. 1996 7 346
138. T. Pastinen A. Kurg A. Metspalu L. Peltonen A. C. Syvanen Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays Genome Res. 1997 7 606
139. P. Hardenbol J. Baner M. Jain M. Nilsson E. A. Namsaraev G. A. Karlin-Neumann H. Fakhrai-Rad M. Ronaghi T. D. Willis U. Landegren R. W. Davis Multiplexed genotyping with sequence-tagged molecular inversion probes Nat. Biotechnol. 2003 21 673
140. D. G. Wang J. B. Fan C. J. Siao A. Berno P. Young R. Sapolsky G. Ghandour N. Perkins E. Winchester J. Spencer L. Kruglyak L. Stein L. Hsie T. Topaloglou E. Hubbell E. Robinson M. Mittmann M. S. Morris N. P. Shen D. Kilburn J. Rioux C. Nusbaum S. Rozen T. J. Hudson R. Lipshutz M. Chee E. S. Lander Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 1998 280 1077
141. L. G. Kostrikis S. Tyagi M. M. Mhlanga D. D. Ho F. R. Kramer Molecular beacons: spectral genotyping of human alleles Science 1998 279 1228
142. M. M. Mhlanga L. Malmberg Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR Methods 2001 25 463
143. E. M. Boon D. M. Ceres T. G. Drummond M. G. Hill J. K. Barton Mutation detection by electrocatalysis at DNA-modified electrodes Nat. Biotechnol. 2000 18 1096
144. M. Inouye R. Ikeda M. Takase T. Tsuri J. Chiba Single-nucleotide polymorphism detection with "wire-like" DNA probes that display quasi "on-off" digital action Proc. Natl. Acad. Sci. U. S. A. 2005 102 11606
145. A. Okamoto K. Kanatani I. Saito Pyrene-labeled base-discriminating fluorescent DNA probes for homogeneous SNP typing J. Am. Chem. Soc. 2004 126 4820
146. A. Okamoto Y. Saito I. Saito Design of base-discriminating fluorescent nucleosides J. Photochem. Photobiol., C 2005 6 108
147. Q. Li G. Luan Q. Guo J. Liang A new class of homogeneous nucleic acid probes based on specific displacement hybridization Nucleic Acids Res. 2002 30 5e
148. W. J. Kim Y. Sato T. Akaike A. Maruyama Cationic comb-type copolymers for DNA analysis Nat. Mater. 2003 2 815
149. A. H. Buck C. J. Campbell P. Dickinson C. P. Mountford H. C. Stoquert J. G. Terry S. A. G. Evans L. M. Keane T.-J. Su A. R. Mount A. J. Walton J. S. Beattie J. Crain P. Ghazal DNA nanoswitch as a biosensor Anal. Chem. 2007 79 4724
150. D. Meserve Z. Wang D. D. Zhang P. K. Wong A double-stranded molecular probe for homogeneous nucleic acid analysis Analyst 2008 133 1013
151. H. K. K. Subramanian B. Chakraborty R. Sha N. C. Seeman The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami Nano Lett. 2011 11 910
152. D. Y. Zhang S. X. Chen P. Yin Optimizing the specificity of nucleic acid hybridization Nat. Chem. 2012 4 208
153. K. Nakatani S. Sando H. Kumasawa J. Kikuchi I. Saito Recognition of guanine-guanine mismatches by the dimeric form of 2-amino-1,8-naphthyridine J. Am. Chem. Soc. 2001 123 12650
154. K. Nakatani S. Sando I. Saito Scanning of guanine-guanine mismatches in DNA by synthetic ligands using surface plasmon resonance Nat. Biotechnol. 2001 19 51
155. A. Kobori S. Horie H. Suda I. Saito K. Nakatani The SPR sensor detecting cytosine-cytosine mismatches J. Am. Chem. Soc. 2004 126 557
156. B. Vogelstein K. W. Kinzler Digital PCR Proc. Natl. Acad. Sci. U. S. A. 1999 96 9236
157. C. L. Ho R. J. Karman R. Dehari T. L. Wang L. M. Shih Mutations of BRAF and KRAS precede the development of ovarian serous borderline tumors Cancer Res. 2004 64 6915
158. H.-C. Yeh Y. P. Ho I. M. Shih T. H. Wang Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis Nucleic Acids Res. 2006 34 e35
159. R. J. Kurman I. M. Shih Pathogenesis of ovarian cancer: lessons from morphology and molecular biology and their clinical implications Int. J. Gynecol. Pathol. 2008 27 151
160. A. Star E. Tu J. Niemann J. C. P. Gabriel C. S. Joiner C. Valcke Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors Proc. Natl. Acad. Sci. U. S. A. 2006 103 921
161. X. B. Zhong R. Reynolds J. R. Kidd K. K. Kidd R. Jenison R. A. Marlar D. C. Ward Single-nucleotide polymorphism genotyping on optical thin-film biosensor chips Proc. Natl. Acad. Sci. U. S. A. 2003 100 11559
162. S. J. Park T. A. Taton C. A. Mirkin Array-based electrical detection of DNA with nanoparticle probes Science 2002 295 1503
163. J. B. de Kok E. T. G. Wiegerinck B. A. J. Giesendorf D. W. Swinkels Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes) Hum. Mutat. 2002 19 554
164. D. M. Kolpashchikov Binary malachite green aptamer for fluorescent detection of nucleic acids J. Am. Chem. Soc. 2005 127 12442
165. Y. Xiao K. J. I. Plakos X. Lou R. J. White J. Qian K. W. Plaxco H. T. Soh Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe Angew. Chem., Int. Ed. 2009 48 4354
166. J. T. Petty B. Sengupta S. P. Story N. N. Degtyareva DNA sensing by amplifying the number of near-infrared emitting, oligonucleotide-encapsulated silver clusters Anal. Chem. 2011 83 5957
167. J. T. Petty C. Fan S. P. Story B. Sengupta A. St. John Iyer Z. Prudowsky R. M. Dickson DNA encapsulation of 10 silver atoms producing a bright, modulatable, near-infrared-emitting cluster J. Phys. Chem. Lett. 2010 1 2524
168. J. T. Petty B. Giri I. C. Miller D. A. Nicholson O. O. Sergev T. M. Banks S. P. Story Silver clusters as both chromophoric reporters and DNA ligands Anal. Chem. 2013 85 2183
169. G. Y. Lan W. Y. Chen H. T. Chang One-pot synthesis of fluorescent oligonucleotide Ag nanoclusters for specific and sensitive detection of DNA Biosens. Bioelectron. 2011 26 2431
170. P. Shah A. Rørvig-Lund S. B. Chaabane P. W. Thulstrup H. G. Kjaergaard E. Fron J. Hofkens S. W. Yang T. Vosch Design aspects of bright red emissive silver nanoclusters/DNA probes for microRNA detection ACS Nano 2012 6 8803
171. S. He B. Song D. Li C. Zhu W. Qi Y. Wen L. Wang S. Song H. Fang C. Fan A graphene nanoprobe for rapid, sensitive, and multicolor fluorescent DNA analysis Adv. Funct. Mater. 2010 20 453
172. K. P. Loh Q. Bao G. Eda M. Chhowalla Graphene oxide as a chemically tunable platform for optical applications Nat. Chem. 2010 2 1015
173. Y. Tao Y. Lin Z. Huang J. Ren X. Qu DNA-templated silver nanoclusters-graphene oxide nanohybrid materials: a platform for label-free and sensitive fluorescence turn-on detection of multiple nucleic acid targets Analyst 2012 137 2588
174. K. Ma Q. Cui G. Liu F. Wu S. Xu Y. Shao DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition Nanotechnology 2011 22 305502
175. S. W. Yang T. Vosch Rapid detection of microRNA by a silver nanocluster DNA probe Anal. Chem. 2011 83 6935
176. Y. Q. Liu M. Zhang B. C. Yin B. C. Ye Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification Anal. Chem. 2012 84 5165
177. H. Dong S. Jin H. Ju K. Hao L. P. Xu H. Lu X. Zhang Trace and label-free microRNA detection using oligonucleotide encapsulated silver nanoclusters as probes Anal. Chem. 2012 84 8670
178. L. Stryer R. P. Haugland Energy transfer: a spectroscopic ruler Proc. Natl. Acad. Sci. U. S. A. 1967 58 719
179. C. S. Yun A. Javier T. Jennings M. Fisher S. Hira S. Peterson B. Hopkins N. O. Reich G. F. Strouse Nanometal surface energy transfer in optical rulers, breaking the FRET barrier J. Am. Chem. Soc. 2005 127 3115
180. H. Yang G. B. Luo P. Karnchanaphanurach T. M. Louie I. Rech S. Cova L. Y. Xun X. S. Xie Protein conformational dynamics probed by single-molecule electron transfer Science 2003 302 262
181. M. Bates T. R. Blosser X. W. Zhuang Short-range spectroscopic ruler based on a single-molecule optical switch Phys. Rev. Lett. 2005 94 108101
182. C. Sonnichsen B. M. Reinhard J. Liphardt A. P. Alivisatos A molecular ruler based on plasmon coupling of single gold and silver nanoparticles Nat. Biotechnol. 2005 23 741
183. S. R. Nicewarner-Pena R. G. Freeman B. D. Reiss L. He D. J. Peña I. D. Walton R. Cromer C. D. Keating M. J. Natan Submicrometer metallic barcodes Science 2001 294 137
184. D. C. Pregibon M. Toner P. S. Doyle Multifunctional encoded particles for high-throughput biomolecule analysis Science 2007 315 1393
185. R. Fan O. Vermesh A. Srivastava B. K. Yen L. Qin H. Ahmad G. A. Kwong C.-C. Liu J. Gould L. Hood Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood Nat. Biotechnol. 2008 26 1373
186. K. Shiroguchi T. Z. Jia P. A. Sims X. S. Xie Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes Proc. Natl. Acad. Sci. U. S. A. 2012 109 1347
187. J.-M. Nam C. S. Thaxton C. A. Mirkin Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins Science 2003 301 1884
188. M. Xiao A. Phong C. Ha T.-F. Chan D. Cai L. Leung E. Wan A. L. Kistler J. L. DeRisi P. R. Selvin Rapid DNA mapping by fluorescent single molecule detection Nucleic Acids Res. 2007 35 e16
189. M. Xiao E. Wan C. Chu W.-C. Hsueh Y. Cao P.-Y. Kwok Direct determination of haplotypes from single DNA molecules Nat. Methods 2009 6 199
190. Y. Li Y. T. H. Cu D. Luo Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes Nat. Biotechnol. 2005 23 885
191. G. K. Geiss R. E. Bumgarner B. Birditt T. Dahl N. Dowidar D. L. Dunaway H. P. Fell S. Ferree R. D. George T. Grogan Direct multiplexed measurement of
192. S. Rauf A. Glidle J. M. Cooper Production of quantum dot barcodes using biological self-assembly Adv. Mater. 2009 21 4020
193. M. Han X. Gao J. Z. Su S. Nie Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules Nat. Biotechnol. 2001 19 631
194. C. Lin R. Jungmann A. M. Leifer C. Li D. Levner G. M. Church W. M. Shih P. Yin Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA Nat. Chem. 2012 4 832
195. C. Sun H. Yang Y. Yuan X. Tian L. Wang Y. Guo L. Xu J. Lei N. Gao G. J. Anderson Controlling assembly of paired gold clusters within apoferritin nanoreactor for in vivo kidney targeting and biomedical imaging J. Am. Chem. Soc. 2011 133 8617
196. S. Pal R. Varghese Z. Deng Z. Zhao A. Kumar H. Yan Y. Liu Site-specific synthesis and in situ immobilization of fluorescent silver nanoclusters on DNA nanoscaffolds by use of the Tollens reaction Angew. Chem. 2011 123 4262
197. L. Feng Z. Huang J. Ren X. Qu Toward site-specific, homogeneous and highly stable fluorescent silver nanoclusters fabrication on triplex DNA scaffolds Nucleic Acids Res. 2012 40 e122
198. D. Schultz E. G. Gwinn Silver atom and strand numbers in fluorescent and dark Ag:DNAs Chem. Commun. 2012 48 5748
199. V. Soto-Verdugo H. Metiu E. Gwinn The properties of small Ag clusters bound to DNA bases J. Chem. Phys. 2010 132 195102
200. S. Goel K. A. Velizhanin A. Piryatinski S. Tretiak S. A. Ivanov DFT study of ligand binding to small gold clusters J. Phys. Chem. Lett. 2010 1 927
201. T. Driehorst P. O'Neill P. M. Goodwin S. Pennathur D. K. Fygenson Distinct conformations of DNA-stabilized fluorescent silver nanoclusters revealed by electrophoretic mobility and diffusivity measurements Langmuir 2011 27 8923
202. P. D. Jadzinsky G. Calero C. J. Ackerson D. A. Bushnell R. D. Kornberg Structure of a thiol monolayer-protected gold nanoparticle at 1.1 Å resolution Science 2007 318 430
203. T.-H. Lee J. I. Gonzalez J. Zheng R. M. Dickson Single-molecule optoelectronics Acc. Chem. Res. 2005 38 534
204. J. Akola M. Walter R. L. Whetten H. Häkkinen H. Grönbeck On the structure of thiolate-protected Au25 J. Am. Chem. Soc. 2008 130 3756
205. E. B. Guidez C. M. Aikens Theoretical analysis of the optical excitation spectra of silver and gold nanowires Nanoscale 2012 4 4190