Abstract

We propose and experimentally demonstrate a new class of sensor for specific DNA sequences based on molecular beacons (MB) immobilized on the internal surfaces of suspended core optical fibers (SCF). MBs, a type of hairpin structured DNA probe, are attached on the surface of the SCF core using a fuzzy nanoassembly process used in conjunction with a biotin-streptavidin-biotin surface attachment strategy. The proposed DNA sensor detects complementary DNA sequences (cDNA) while discriminating sequences differing from the target by just one base. This enables the detection of DNA in unprecedentedly small sample volumes (nL scale) and is, to the best of our knowledge, the first specific DNA detection using a DNA probe immobilized within a microstructured optical fiber.

© 2012 OSA

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2012 (1)

2011 (1)

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

2010 (4)

S. C. Warren-Smith, E. Sinchenko, P. R. Stoddart, and T. M. Monro, “Distributed fluorescence sensing using exposed-core microstructured optical fiber,” IEEE Photon. Technol. Lett.22(18), 1385–1387 (2010).
[CrossRef]

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

S. Sforza, R. Corradini, T. Tedeschi, and R. Marchelli, “Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies,” Chem. Soc. Rev.40(1), 221–232 (2010).
[CrossRef] [PubMed]

2009 (2)

2008 (2)

2007 (1)

2006 (2)

2000 (1)

X. Liu, W. Farmerie, S. Schuster, and W. Tan, “Molecular beacons for DNA biosensors with Micrometer to Submicrometer dimensions,” Anal. Biochem.283(1), 56–63 (2000).
[CrossRef] [PubMed]

1999 (1)

X. Liu and W. Tan, “A Fiber-Optic Evanescent Wave DNA Biosensor Based on Novel Molecular Beacons,” Anal. Chem.71(22), 5054–5059 (1999).
[CrossRef] [PubMed]

1998 (2)

J. C. Knight, J. Broeng, T. A. Birks, and P. S. J. Russell, “Photonic band gap guidance in optical fibers,” Science282(5393), 1476–1478 (1998).
[CrossRef] [PubMed]

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

1997 (1)

G. Decher, “Fuzzy Nanoassemblies: Toward layered polymeric multicomposites,” Science277(5330), 1232–1237 (1997).
[CrossRef]

1996 (1)

S. Tyagi and F. R. Kramer, “Molecular Beacons: Probes that Fluoresce upon Hybridization,” Nat. Biotechnol.14(3), 303–308 (1996).
[CrossRef] [PubMed]

Abell, A. D.

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

Afshar, S.

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Bang, O.

Bennion, I.

Berno, A.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Birks, T. A.

J. C. Knight, J. Broeng, T. A. Birks, and P. S. J. Russell, “Photonic band gap guidance in optical fibers,” Science282(5393), 1476–1478 (1998).
[CrossRef] [PubMed]

Broeng, J.

J. C. Knight, J. Broeng, T. A. Birks, and P. S. J. Russell, “Photonic band gap guidance in optical fibers,” Science282(5393), 1476–1478 (1998).
[CrossRef] [PubMed]

Chee, M.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Chen, X.

Cooper, K. L.

Corradini, R.

S. Sforza, R. Corradini, T. Tedeschi, and R. Marchelli, “Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies,” Chem. Soc. Rev.40(1), 221–232 (2010).
[CrossRef] [PubMed]

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Coscelli, E.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Cucinotta, A.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Davies, E.

Decher, G.

G. Decher, “Fuzzy Nanoassemblies: Toward layered polymeric multicomposites,” Science277(5330), 1232–1237 (1997).
[CrossRef]

Dufva, M.

Ebendorff-Heidepriem, H.

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Y. Ruan, T. C. Foo, S. C. Warren-Smith, P. Hoffmann, R. C. Moore, H. Ebendorff-Heidepriem, and T. M. Monro, “Antibody immobilization within glass microstructured fibers: a route to sensitive and selective biosensors,” Opt. Express16(22), 18514–18523 (2008).
[CrossRef] [PubMed]

Fan, J. B.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Farmerie, W.

X. Liu, W. Farmerie, S. Schuster, and W. Tan, “Molecular beacons for DNA biosensors with Micrometer to Submicrometer dimensions,” Anal. Biochem.283(1), 56–63 (2000).
[CrossRef] [PubMed]

Foo, T. C.

François, A.

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Gawlik, W.

Ghandour, G.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Grabka, M.

Han, Y.-G.

Heng, S.

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Hine, A.

Hoffmann, P.

Høiby, P. E.

Hsie, L.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Hubbell, E.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Hudson, T. J.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Hughes, M.

Jang, H. S.

Jensen, J. B.

Kilburn, D.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Kim, J. P.

Knight, J. C.

J. C. Knight, J. Broeng, T. A. Birks, and P. S. J. Russell, “Photonic band gap guidance in optical fibers,” Science282(5393), 1476–1478 (1998).
[CrossRef] [PubMed]

Kramer, F. R.

S. Tyagi and F. R. Kramer, “Molecular Beacons: Probes that Fluoresce upon Hybridization,” Nat. Biotechnol.14(3), 303–308 (1996).
[CrossRef] [PubMed]

Kruglyak, L.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Kwon, O. J.

Lander, E. S.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Lee, K. S.

Lipshutz, R.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Liu, X.

X. Liu, W. Farmerie, S. Schuster, and W. Tan, “Molecular beacons for DNA biosensors with Micrometer to Submicrometer dimensions,” Anal. Biochem.283(1), 56–63 (2000).
[CrossRef] [PubMed]

X. Liu and W. Tan, “A Fiber-Optic Evanescent Wave DNA Biosensor Based on Novel Molecular Beacons,” Anal. Chem.71(22), 5054–5059 (1999).
[CrossRef] [PubMed]

Marchelli, R.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

S. Sforza, R. Corradini, T. Tedeschi, and R. Marchelli, “Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies,” Chem. Soc. Rev.40(1), 221–232 (2010).
[CrossRef] [PubMed]

Mergo, P.

Mittmann, M.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Monro, T. M.

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

S. C. Warren-Smith, E. Sinchenko, P. R. Stoddart, and T. M. Monro, “Distributed fluorescence sensing using exposed-core microstructured optical fiber,” IEEE Photon. Technol. Lett.22(18), 1385–1387 (2010).
[CrossRef]

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Y. Ruan, T. C. Foo, S. C. Warren-Smith, P. Hoffmann, R. C. Moore, H. Ebendorff-Heidepriem, and T. M. Monro, “Antibody immobilization within glass microstructured fibers: a route to sensitive and selective biosensors,” Opt. Express16(22), 18514–18523 (2008).
[CrossRef] [PubMed]

Moore, R. C.

Morris, M. S.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Nusbaum, C.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Park, K. N.

Passaro, D.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Pedersen, L. H.

Perkins, N.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Poli, F.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Pustelny, S.

Rindorf, L.

Rioux, J.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Robinson, E.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Rozen, S.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Ruan, Y.

Russell, P. S. J.

J. C. Knight, J. Broeng, T. A. Birks, and P. S. J. Russell, “Photonic band gap guidance in optical fibers,” Science282(5393), 1476–1478 (1998).
[CrossRef] [PubMed]

Sapolsky, R.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Schartner, E. P.

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Schuster, S.

X. Liu, W. Farmerie, S. Schuster, and W. Tan, “Molecular beacons for DNA biosensors with Micrometer to Submicrometer dimensions,” Anal. Biochem.283(1), 56–63 (2000).
[CrossRef] [PubMed]

Selleri, S.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Sforza, S.

S. Sforza, R. Corradini, T. Tedeschi, and R. Marchelli, “Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies,” Chem. Soc. Rev.40(1), 221–232 (2010).
[CrossRef] [PubMed]

Shen, N.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Siao, C. J.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Sim, S. J.

Sinchenko, E.

S. C. Warren-Smith, E. Sinchenko, P. R. Stoddart, and T. M. Monro, “Distributed fluorescence sensing using exposed-core microstructured optical fiber,” IEEE Photon. Technol. Lett.22(18), 1385–1387 (2010).
[CrossRef]

Sozzi, M.

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

Spencer, J.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Stein, L.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Stoddart, P. R.

S. C. Warren-Smith, E. Sinchenko, P. R. Stoddart, and T. M. Monro, “Distributed fluorescence sensing using exposed-core microstructured optical fiber,” IEEE Photon. Technol. Lett.22(18), 1385–1387 (2010).
[CrossRef]

Sugden, K.

Tan, W.

X. Liu, W. Farmerie, S. Schuster, and W. Tan, “Molecular beacons for DNA biosensors with Micrometer to Submicrometer dimensions,” Anal. Biochem.283(1), 56–63 (2000).
[CrossRef] [PubMed]

X. Liu and W. Tan, “A Fiber-Optic Evanescent Wave DNA Biosensor Based on Novel Molecular Beacons,” Anal. Chem.71(22), 5054–5059 (1999).
[CrossRef] [PubMed]

Tedeschi, T.

S. Sforza, R. Corradini, T. Tedeschi, and R. Marchelli, “Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies,” Chem. Soc. Rev.40(1), 221–232 (2010).
[CrossRef] [PubMed]

Topaloglou, T.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Tyagi, S.

S. Tyagi and F. R. Kramer, “Molecular Beacons: Probes that Fluoresce upon Hybridization,” Nat. Biotechnol.14(3), 303–308 (1996).
[CrossRef] [PubMed]

Walt, D. R.

D. R. Walt, “Fibre Optic Microarrays,” Chem. Soc. Rev.39(1), 38–50 (2009).
[CrossRef] [PubMed]

Wang, A.

Wang, D. G.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Wang, Y.

Warren-Smith, S. C.

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

S. C. Warren-Smith, E. Sinchenko, P. R. Stoddart, and T. M. Monro, “Distributed fluorescence sensing using exposed-core microstructured optical fiber,” IEEE Photon. Technol. Lett.22(18), 1385–1387 (2010).
[CrossRef]

Y. Ruan, T. C. Foo, S. C. Warren-Smith, P. Hoffmann, R. C. Moore, H. Ebendorff-Heidepriem, and T. M. Monro, “Antibody immobilization within glass microstructured fibers: a route to sensitive and selective biosensors,” Opt. Express16(22), 18514–18523 (2008).
[CrossRef] [PubMed]

Winchester, E.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Wolfbeis, O. S.

O. S. Wolfbeis, “Fiber-Optic Chemical Sensors and Biosensors,” Anal. Chem.78(12), 3859–3874 (2006).
[CrossRef] [PubMed]

Young, P.

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Zhang, L.

Zhou, K.

Anal. Biochem. (1)

X. Liu, W. Farmerie, S. Schuster, and W. Tan, “Molecular beacons for DNA biosensors with Micrometer to Submicrometer dimensions,” Anal. Biochem.283(1), 56–63 (2000).
[CrossRef] [PubMed]

Anal. Chem. (2)

O. S. Wolfbeis, “Fiber-Optic Chemical Sensors and Biosensors,” Anal. Chem.78(12), 3859–3874 (2006).
[CrossRef] [PubMed]

X. Liu and W. Tan, “A Fiber-Optic Evanescent Wave DNA Biosensor Based on Novel Molecular Beacons,” Anal. Chem.71(22), 5054–5059 (1999).
[CrossRef] [PubMed]

Chem. Soc. Rev. (2)

D. R. Walt, “Fibre Optic Microarrays,” Chem. Soc. Rev.39(1), 38–50 (2009).
[CrossRef] [PubMed]

S. Sforza, R. Corradini, T. Tedeschi, and R. Marchelli, “Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies,” Chem. Soc. Rev.40(1), 221–232 (2010).
[CrossRef] [PubMed]

IEEE Photon. Technol. Lett. (1)

S. C. Warren-Smith, E. Sinchenko, P. R. Stoddart, and T. M. Monro, “Distributed fluorescence sensing using exposed-core microstructured optical fiber,” IEEE Photon. Technol. Lett.22(18), 1385–1387 (2010).
[CrossRef]

IEEE Sel. Top. Quantum. Electron. (1)

E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, S. Selleri, R. Corradini, and R. Marchelli, “Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers,” IEEE Sel. Top. Quantum. Electron.16(4), 967–972 (2010).
[CrossRef]

J. Lightwave Technol. (1)

Langmuir (1)

S. C. Warren-Smith, S. Heng, H. Ebendorff-Heidepriem, A. D. Abell, and T. M. Monro, “Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber,” Langmuir27(9), 5680–5685 (2011).
[CrossRef] [PubMed]

Nat. Biotechnol. (1)

S. Tyagi and F. R. Kramer, “Molecular Beacons: Probes that Fluoresce upon Hybridization,” Nat. Biotechnol.14(3), 303–308 (1996).
[CrossRef] [PubMed]

Opt. Express (4)

Opt. Fiber Technol. (1)

T. M. Monro, S. C. Warren-Smith, E. P. Schartner, A. François, S. Heng, H. Ebendorff-Heidepriem, and S. Afshar, “Sensing with suspended-core optical fibers,” Opt. Fiber Technol.16(6), 343–356 (2010).
[CrossRef]

Opt. Lett. (1)

Science (3)

J. C. Knight, J. Broeng, T. A. Birks, and P. S. J. Russell, “Photonic band gap guidance in optical fibers,” Science282(5393), 1476–1478 (1998).
[CrossRef] [PubMed]

G. Decher, “Fuzzy Nanoassemblies: Toward layered polymeric multicomposites,” Science277(5330), 1232–1237 (1997).
[CrossRef]

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. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, “Large-scale Identification, Mapping, and Genotyping of Single-nucleotide polymorphisms in the human genome,” Science280(5366), 1077–1082 (1998).
[CrossRef] [PubMed]

Other (3)

Y. Yanina, Shevchenko, David A. Blair, Maria C. Derosa, and Jacques Albert, “DNA Target Detection Using Gold-Coated Tilted Fiber Bragg Gratings in Aqueous Media,” in Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science and Photonic Applications Systems Technologies, Technical Digest (CD) (Optical Society of America, 2008), paper CMJ4.

Y. Sun, and X. Fan, “Highly Selective Single-Nucleotide Polymorphism Detection with Optofluidic Ring Resonator Lasers,” in CLEO - Laser Applications to Photonic Applications, Technical Digest (CD) (Optical Society of America, 2011), paper CWL6.

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Figures (4)

Fig. 1
Fig. 1

(a) A scanning electron microscope (SEM) image of the cross-section of the SCF used in the functionalization experiment and the schematic diagram of the final surface state of the MB functionalized SCF and (b) Molecular beacons go through conformational change upon hybridizing with cDNA while remaining in closed form upon hybridizing with nDNA

Fig. 2
Fig. 2

Experiment setup for fluorescence measurement of the immobilized SCF filled with DNA solutions

Fig. 3
Fig. 3

Fluorescence enhancements of the MB functionalized fiber and that of the control fiber upon hybridization with cDNA.

Fig. 4
Fig. 4

(a) Fluorescence enhancement of the MB functionalized SCF upon filling with buffer solutions containing cDNA, oDNA, nDNA or buffer only (see legend) and (b) Integrated and normalized fluorescence enhancements with error bars for three consecutive measurements.

Tables (1)

Tables Icon

Table 1 Molecular Beacons and DNA Sequences used for Testing the Immobilized SCFa

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