Abstract

Surface enhanced Raman spectroscopy (SERS) is a selective and sensitive technique, which allows for the detection of protease activity by monitoring the cleavage of peptide substrates. Commonly used free-space based SERS substrates, however, require the use of bulky and expensive instrumentation, limiting their use to laboratory environments. An integrated photonics approach aims to implement various free-space optical components to a reliable, mass-reproducible and cheap photonic chip. We here demonstrate integrated SERS detection of trypsin activity using a nanoplasmonic slot waveguide as a waveguide-based SERS substrate. Despite the continuously improving SERS performance of the waveguide-based SERS substrates, they currently still do not reach the SERS enhancements of free-space substrates. To mitigate this, we developed an improved peptide substrate in which we incorporated the non-natural aromatic amino acid 4-cyano-phenylalanine, which provides a high intrinsic SERS signal. The use of non-natural aromatics is expected to extend the possibilities for multiplexing measurements, where the activity of several proteases can be detected simultaneously.

© 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
  45. X. Nie, E. Ryckeboer, G. Roelkens, and R. Baets, “CMOS-compatible broadband co-propagative stationary Fourier transform spectrometer integrated on a silicon nitride photonics platform,” Opt. Express 25(8), A409–A418 (2017).
    [Crossref]
  46. J. C. Powers, J. L. Asgian, Ö. Doǧan Ekici, and K. Ellis James, “Irreversible Inhibitors of Serine, Cysteine, and Threonine Proteases,” Chem. Rev. 102(12), 4639–4750 (2002).
    [Crossref]
  47. M. Tabatabaei, A. Sangar, N. Kazemi-Zanjani, P. Torchio, A. Merlen, and F. Lagugné-Labarthet, “Optical Properties of Silver and Gold Tetrahedral Nanopyramid Arrays Prepared by Nanosphere Lithography,” J. Phys. Chem. C 117(28), 14778–14786 (2013).
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    [Crossref]

2020 (2)

2019 (4)

2018 (4)

F. Peyskens, P. Wuytens, A. Raza, P. Van Dorpe, and R. Baets, “Waveguide excitation and collection of surface-enhanced Raman scattering from a single plasmonic antenna,” Nanophotonics 7(7), 1299–1306 (2018).
[Crossref]

A. Raza, S. Clemmen, P. Wuytens, M. Muneeb, M. Van Daele, J. Dendooven, C. Detavernier, A. Skirtach, and R. Baets, “ALD assisted nanoplasmonic slot waveguide for on-chip Enhanced Raman Spectroscopy,” APL Photonics 3(11), 116105 (2018).
[Crossref]

H. M. K. Wong, M. K. Dezfouli, L. Sun, S. Hughes, and A. S. Helmy, “Nanoscale Plasmonic Slot Waveguides for Enhanced Raman Spectroscopy,” Phys. Rev. B 98(8), 085124 (2018).
[Crossref]

Q. Cao, J. Feng, H. Lu, H. Zhang, F. Zhang, and H. Zeng, “Surface-enhanced Raman scattering using nanoporous gold on suspended silicon nitride waveguides,” Opt. Express 26(19), 24614–24620 (2018).
[Crossref]

2017 (5)

P. C. Wuytens, A. G. Skirtach, and R. Baets, “On-Chip Surface-Enhanced Raman Spectroscopy using Nanosphere-Lithography Patterned Antennas on Silicon Nitride Waveguides,” Opt. Express 25(11), 12926–12934 (2017).
[Crossref]

A. Dhakal, P. Wuytens, A. Raza, N. Le Thomas, and R. Baets, “Silicon Nitride Background in Nanophotonic Waveguide Enhanced Raman Spectroscopy,” Materials 10(2), 140 (2017).
[Crossref]

I. L. H. Ong and K.-L. Yang, “Recent developments in protease activity assays and sensors,” Analyst 142(11), 1867–1881 (2017).
[Crossref]

P. C. Wuytens, H. Demol, N. Turk, K. Gevaert, A. Skirtach, M. Lamkanfi, and R. Baets, “Gold nanodome SERS platform for label-free detection of protease activity,” Faraday Discuss. 205, 345–361 (2017).
[Crossref]

X. Nie, E. Ryckeboer, G. Roelkens, and R. Baets, “CMOS-compatible broadband co-propagative stationary Fourier transform spectrometer integrated on a silicon nitride photonics platform,” Opt. Express 25(8), A409–A418 (2017).
[Crossref]

2016 (6)

E. Gizem, M. Hedström, and B. Mattiasson, “A sensitive and real-time assay of trypsin by using molecular imprinting-based capacitive biosensor,” Biosens. Bioelectron. 86, 557–565 (2016).
[Crossref]

A. N. Ramya, M. M. Joseph, J. B. Nair, V. Karunakaran, N. Narayanan, and K. K. Maiti, “New Insight of Tetraphenylethylene-based Raman Signatures for Targeted SERS Nanoprobe Construction Toward Prostate Cancer Cell Detection,” ACS Appl. Mater. Interfaces 8(16), 10220–10225 (2016).
[Crossref]

A. Dhakal, C. Wuytens, F. Peyskens, K. Jans, N. Le Thomas, and R. Baets, “Nanophotonic waveguide enhanced Raman spectroscopy of biological submonolayers,” ACS Photonics 3(11), 2141–2149 (2016).
[Crossref]

S. A. Holmstrom, T. H. Stievater, D. A. Kozak, M. W. Pruessner, N. Tyndall, W. S. Rabinovich, R. A. McGill, and J. B. Khurgin, “Trace gas Raman spectroscopy using functionalized waveguides,” Optica 3(8), 891–896 (2016).
[Crossref]

F. Peyskens, A. Dhakal, P. Van Dorpe, N. Le Thomas, and R. Baets, “Surface Enhanced Raman Spectroscopy Using a Single Mode Nanophotonic-Plasmonic Platform,” ACS Photonics 3(1), 102–108 (2016).
[Crossref]

F. Tang, P.-M. Adam, and S. Boutami, “Theoretical investigation of SERS nanosensors based on hybrid waveguides made of metallic slots and dielectric strips,” Opt. Express 24(19), 21244–21255 (2016).
[Crossref]

2015 (5)

A. Z. Subramanian, E. Ryckeboer, A. Dhakal, F. Peyskens, A. Malik, B. Kuyken, H. Zhao, S. Pathak, A. Ruocco, A. D. Groote, P. Wuytens, D. Martens, F. Leo, W. Xie, U. D. Dave, M. Muneeb, P. V. Dorpe, J. V. Campenhout, W. Bogaerts, P. Bienstman, N. L. Thomas, D. V. Thourhout, Z. Hens, G. Roelkens, and R. Baets, “Silicon and silicon nitride photonic circuits forspectroscopic sensing on-a-chip,” Photonics Res. 3(5), B47–B59 (2015).
[Crossref]

Z. Wu, Y. Liu, Y. Liu, H. Xiao, A. Shen, X. Zhou, and J. Hu, “A simple and universal “turn-on” detection platform for proteases based on surface enhanced Raman scattering (SERS),” Biosens. Bioelectron. 65, 375–381 (2015).
[Crossref]

A. Dhakal, A. Raza, F. Peyskens, A. Z. Subramanian, S. Clemmen, N. Le Thomas, and R. Baets, “Efficiency of evanescent excitation and collection of spontaneous Raman scattering near high index contrast channel waveguides,” Opt. Express 23(21), 27391–27404 (2015).
[Crossref]

Y. Lai, S. Sun, T. He, S. Schlücker, and Y. Wang, “Raman-encoded microbeads for spectral multiplexing with SERS detection,” RSC Adv. 5(18), 13762–13767 (2015).
[Crossref]

E. P. Haglund, S. Kumari, P. Westbergh, J. S. Gustavsson, G. Roelkens, R. Baets, and A. Larsson, “Silicon-integrated short-wavelength hybrid-cavity VCSEL,” Opt. Express 23(26), 33634–33640 (2015).
[Crossref]

2014 (1)

2013 (4)

L. Chen, X. Fu, and J. Li, “Ultrasensitive surface-enhanced Raman scattering detection of trypsin based on anti-aggregation of 4-mercaptopyridine-functionalized silver nanoparticles: an optical sensing platform toward proteases,” Nanoscale 5(13), 5905–5911 (2013).
[Crossref]

Z. Wu, Y. Liu, X. Zhou, A. Shen, and J. Hu, “A “turn-off” SERS-based detection platform for ultrasensitive detection of thrombin based on enzymatic assays,” Biosens. Bioelectron. 44, 10–15 (2013).
[Crossref]

E. Vandermarliere, M. Michael, and M. Lennart, “Getting intimate with trypsin, the leading protease in proteomics,” Mass Spectrom. Rev. 32(6), 453–465 (2013).
[Crossref]

M. Tabatabaei, A. Sangar, N. Kazemi-Zanjani, P. Torchio, A. Merlen, and F. Lagugné-Labarthet, “Optical Properties of Silver and Gold Tetrahedral Nanopyramid Arrays Prepared by Nanosphere Lithography,” J. Phys. Chem. C 117(28), 14778–14786 (2013).
[Crossref]

2012 (2)

L. Hu, S. Han, S. Parveen, Y. Yuan, L. Zhang, and G. Xua, “Highly sensitive fluorescent detection of trypsin based on BSA-stabilized gold nanoclusters,” Biosens. Bioelectron. 32(1), 297–299 (2012).
[Crossref]

H. Häkkinen, “The gold-sulfur interface at the nanoscale,” Nat. Chem. 4(6), 443–455 (2012).
[Crossref]

2011 (2)

G. Zhu, X. Zhu, Q. Fan, and X. Wan, “Raman spectra of amino acids and their aqueous solutions,” Spectrochim. Acta, Part A 78(3), 1187–1195 (2011).
[Crossref]

K. Welser, R. Adsley, B. M. Moore, W. C. Chan, and J. W. Aylott, “Protease sensing with nanoparticle based platforms,” Analyst 136(1), 29–41 (2011).
[Crossref]

2010 (2)

M. Drag and G. S. Salvesen, “Emerging principles in protease-based drug discovery,” Nat. Rev. Drug Discovery 9(9), 690–701 (2010).
[Crossref]

C. Sun, K.-H. Su, J. Valentine, Y. T. Rosa-Bauza, J. A. Ellman, O. Elboudwarej, B. Mukherjee, C. S. Craik, M. A. Shuman, F. F. Chen, and X. Zhang, “Time-Resolved Single-Step Protease Activity Quantification Using Nanoplasmonic Resonator Sensors,” ACS Nano 4(2), 978–984 (2010).
[Crossref]

2009 (1)

H. P. Erickson, “Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy,” Biol. Proced. Online 11(1), 32–51 (2009).
[Crossref]

2008 (2)

C. L. Weeks, A. Polishchuk, Z. Getahun, W. F. DeGrado, and T. G. Spiro, “Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the νC≡N band of 4-cyanophenylalanine,” J. Raman Spectrosc. 39(11), 1606–1613 (2008).
[Crossref]

F. Wei, D. Zhang, N. J. Halas, and J. D. Hartgerink, “Aromatic Amino Acids Providing Characteristic Motifs in the Raman and SERS Spectroscopy of Peptides,” J. Phys. Chem. B 112(30), 9158–9164 (2008).
[Crossref]

2006 (1)

B. Turk, “Targeting proteases: successes, failures and future prospects,” Nat. Rev. Drug Discovery 5(9), 785–799 (2006).
[Crossref]

2005 (1)

C. Flexner, G. Bate, and P. Kirkpatrick, “Tripnavir,” Nat. Rev. Drug Discovery 4(12), 955–956 (2005).
[Crossref]

2004 (1)

R. Lévy, N. T. K. Thanh, R. C. Doty, I. Hussain, R. J. Nichols, D. J. Schiffrin, M. Brust, and D. G. Fernig, “Rational and Combinatorial Design of Peptide Capping Ligands for Gold Nanoparticles,” J. Am. Chem. Soc. 126(32), 10076–10084 (2004).
[Crossref]

2003 (1)

C. G. Smith and J. R. Vane, “The Discovery of Captopril,” FASEB J. 17(8), 788–789 (2003).
[Crossref]

2002 (2)

W. F. Patton, “Detection technologies in proteome analysis,” J. Chromatogr. B: Anal. Technol. Biomed. Life Sci. 771(1-2), 3–31 (2002).
[Crossref]

J. C. Powers, J. L. Asgian, Ö. Doǧan Ekici, and K. Ellis James, “Irreversible Inhibitors of Serine, Cysteine, and Threonine Proteases,” Chem. Rev. 102(12), 4639–4750 (2002).
[Crossref]

1985 (1)

M. Moskovits, “Surface-enhanced spectroscopy,” Rev. Mod. Phys. 57(3), 783–826 (1985).
[Crossref]

Adam, P.-M.

Adsley, R.

K. Welser, R. Adsley, B. M. Moore, W. C. Chan, and J. W. Aylott, “Protease sensing with nanoparticle based platforms,” Analyst 136(1), 29–41 (2011).
[Crossref]

Asgian, J. L.

J. C. Powers, J. L. Asgian, Ö. Doǧan Ekici, and K. Ellis James, “Irreversible Inhibitors of Serine, Cysteine, and Threonine Proteases,” Chem. Rev. 102(12), 4639–4750 (2002).
[Crossref]

Aylott, J. W.

K. Welser, R. Adsley, B. M. Moore, W. C. Chan, and J. W. Aylott, “Protease sensing with nanoparticle based platforms,” Analyst 136(1), 29–41 (2011).
[Crossref]

Baets, R.

N. Turk, A. Raza, P. Wuytens, H. Demol, M. Van Daele, C. Detavernier, A. Skirtach, K. Gevaert, and R. Baets, “Comparison of Free-Space and Waveguide-Based SERS Platforms,” Nanomaterials 9(10), 1401 (2019).
[Crossref]

A. Raza, S. Clemmen, P. Wuytens, M. de Goede, A. S. K. Tong, N. Le Thomas, C. Liu, J. Suntivich, A. G. Skirtach, S. M. Garcia-Blanco, D. J. Blumenthal, J. S. Wilkinson, and R. Baets, “High index contrast photonic platforms for on-chip Raman spectroscopy,” Opt. Express 27(16), 23067–23079 (2019).
[Crossref]

X. Nie, N. Turk, Y. Li, Z. Liu, and R. Baets, “High extinction ratio on-chip pump-rejection filter based on cascaded grating-assisted contra-directional couplers in silicon nitride rib waveguides,” Opt. Lett. 44(9), 2310–2313 (2019).
[Crossref]

A. Raza, S. Clemmen, P. Wuytens, M. Muneeb, M. Van Daele, J. Dendooven, C. Detavernier, A. Skirtach, and R. Baets, “ALD assisted nanoplasmonic slot waveguide for on-chip Enhanced Raman Spectroscopy,” APL Photonics 3(11), 116105 (2018).
[Crossref]

F. Peyskens, P. Wuytens, A. Raza, P. Van Dorpe, and R. Baets, “Waveguide excitation and collection of surface-enhanced Raman scattering from a single plasmonic antenna,” Nanophotonics 7(7), 1299–1306 (2018).
[Crossref]

A. Dhakal, P. Wuytens, A. Raza, N. Le Thomas, and R. Baets, “Silicon Nitride Background in Nanophotonic Waveguide Enhanced Raman Spectroscopy,” Materials 10(2), 140 (2017).
[Crossref]

P. C. Wuytens, H. Demol, N. Turk, K. Gevaert, A. Skirtach, M. Lamkanfi, and R. Baets, “Gold nanodome SERS platform for label-free detection of protease activity,” Faraday Discuss. 205, 345–361 (2017).
[Crossref]

X. Nie, E. Ryckeboer, G. Roelkens, and R. Baets, “CMOS-compatible broadband co-propagative stationary Fourier transform spectrometer integrated on a silicon nitride photonics platform,” Opt. Express 25(8), A409–A418 (2017).
[Crossref]

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F. Peyskens, P. Wuytens, A. Raza, P. Van Dorpe, and R. Baets, “Waveguide excitation and collection of surface-enhanced Raman scattering from a single plasmonic antenna,” Nanophotonics 7(7), 1299–1306 (2018).
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F. Peyskens, A. Dhakal, P. Van Dorpe, N. Le Thomas, and R. Baets, “Surface Enhanced Raman Spectroscopy Using a Single Mode Nanophotonic-Plasmonic Platform,” ACS Photonics 3(1), 102–108 (2016).
[Crossref]

Vandermarliere, E.

E. Vandermarliere, M. Michael, and M. Lennart, “Getting intimate with trypsin, the leading protease in proteomics,” Mass Spectrom. Rev. 32(6), 453–465 (2013).
[Crossref]

Vane, J. R.

C. G. Smith and J. R. Vane, “The Discovery of Captopril,” FASEB J. 17(8), 788–789 (2003).
[Crossref]

Verhamme, I. M.

I. M. Verhamme, S. E. Leonard, and R. C. Perkins, “Proteases: Pivot Points in Functional Proteomics,” in Functional Proteomics Methods and Protocols, 313–392 (Humana Press, New York, 2018).

Wan, X.

G. Zhu, X. Zhu, Q. Fan, and X. Wan, “Raman spectra of amino acids and their aqueous solutions,” Spectrochim. Acta, Part A 78(3), 1187–1195 (2011).
[Crossref]

Wang, Y.

Y. Lai, S. Sun, T. He, S. Schlücker, and Y. Wang, “Raman-encoded microbeads for spectral multiplexing with SERS detection,” RSC Adv. 5(18), 13762–13767 (2015).
[Crossref]

Weeks, C. L.

C. L. Weeks, A. Polishchuk, Z. Getahun, W. F. DeGrado, and T. G. Spiro, “Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the νC≡N band of 4-cyanophenylalanine,” J. Raman Spectrosc. 39(11), 1606–1613 (2008).
[Crossref]

Wei, F.

F. Wei, D. Zhang, N. J. Halas, and J. D. Hartgerink, “Aromatic Amino Acids Providing Characteristic Motifs in the Raman and SERS Spectroscopy of Peptides,” J. Phys. Chem. B 112(30), 9158–9164 (2008).
[Crossref]

Welser, K.

K. Welser, R. Adsley, B. M. Moore, W. C. Chan, and J. W. Aylott, “Protease sensing with nanoparticle based platforms,” Analyst 136(1), 29–41 (2011).
[Crossref]

Westbergh, P.

Wilkinson, J. S.

Wong, H. M. K.

H. M. K. Wong, M. K. Dezfouli, L. Sun, S. Hughes, and A. S. Helmy, “Nanoscale Plasmonic Slot Waveguides for Enhanced Raman Spectroscopy,” Phys. Rev. B 98(8), 085124 (2018).
[Crossref]

Wu, Z.

Z. Wu, Y. Liu, Y. Liu, H. Xiao, A. Shen, X. Zhou, and J. Hu, “A simple and universal “turn-on” detection platform for proteases based on surface enhanced Raman scattering (SERS),” Biosens. Bioelectron. 65, 375–381 (2015).
[Crossref]

Z. Wu, Y. Liu, X. Zhou, A. Shen, and J. Hu, “A “turn-off” SERS-based detection platform for ultrasensitive detection of thrombin based on enzymatic assays,” Biosens. Bioelectron. 44, 10–15 (2013).
[Crossref]

Wuytens, C.

A. Dhakal, C. Wuytens, F. Peyskens, K. Jans, N. Le Thomas, and R. Baets, “Nanophotonic waveguide enhanced Raman spectroscopy of biological submonolayers,” ACS Photonics 3(11), 2141–2149 (2016).
[Crossref]

Wuytens, P.

N. Turk, A. Raza, P. Wuytens, H. Demol, M. Van Daele, C. Detavernier, A. Skirtach, K. Gevaert, and R. Baets, “Comparison of Free-Space and Waveguide-Based SERS Platforms,” Nanomaterials 9(10), 1401 (2019).
[Crossref]

A. Raza, S. Clemmen, P. Wuytens, M. de Goede, A. S. K. Tong, N. Le Thomas, C. Liu, J. Suntivich, A. G. Skirtach, S. M. Garcia-Blanco, D. J. Blumenthal, J. S. Wilkinson, and R. Baets, “High index contrast photonic platforms for on-chip Raman spectroscopy,” Opt. Express 27(16), 23067–23079 (2019).
[Crossref]

F. Peyskens, P. Wuytens, A. Raza, P. Van Dorpe, and R. Baets, “Waveguide excitation and collection of surface-enhanced Raman scattering from a single plasmonic antenna,” Nanophotonics 7(7), 1299–1306 (2018).
[Crossref]

A. Raza, S. Clemmen, P. Wuytens, M. Muneeb, M. Van Daele, J. Dendooven, C. Detavernier, A. Skirtach, and R. Baets, “ALD assisted nanoplasmonic slot waveguide for on-chip Enhanced Raman Spectroscopy,” APL Photonics 3(11), 116105 (2018).
[Crossref]

A. Dhakal, P. Wuytens, A. Raza, N. Le Thomas, and R. Baets, “Silicon Nitride Background in Nanophotonic Waveguide Enhanced Raman Spectroscopy,” Materials 10(2), 140 (2017).
[Crossref]

A. Z. Subramanian, E. Ryckeboer, A. Dhakal, F. Peyskens, A. Malik, B. Kuyken, H. Zhao, S. Pathak, A. Ruocco, A. D. Groote, P. Wuytens, D. Martens, F. Leo, W. Xie, U. D. Dave, M. Muneeb, P. V. Dorpe, J. V. Campenhout, W. Bogaerts, P. Bienstman, N. L. Thomas, D. V. Thourhout, Z. Hens, G. Roelkens, and R. Baets, “Silicon and silicon nitride photonic circuits forspectroscopic sensing on-a-chip,” Photonics Res. 3(5), B47–B59 (2015).
[Crossref]

A. Dhakal, A. Z. Subramanian, P. Wuytens, F. Peyskens, N. Le Thomas, and R. Baets, “Evanescent excitation and collection of spontaneous Raman spectra using silicon nitride nanophotonic waveguides,” Opt. Lett. 39(13), 4025–4028 (2014).
[Crossref]

Wuytens, P. C.

P. C. Wuytens, H. Demol, N. Turk, K. Gevaert, A. Skirtach, M. Lamkanfi, and R. Baets, “Gold nanodome SERS platform for label-free detection of protease activity,” Faraday Discuss. 205, 345–361 (2017).
[Crossref]

P. C. Wuytens, A. G. Skirtach, and R. Baets, “On-Chip Surface-Enhanced Raman Spectroscopy using Nanosphere-Lithography Patterned Antennas on Silicon Nitride Waveguides,” Opt. Express 25(11), 12926–12934 (2017).
[Crossref]

Xia, L.

Xiao, H.

Z. Wu, Y. Liu, Y. Liu, H. Xiao, A. Shen, X. Zhou, and J. Hu, “A simple and universal “turn-on” detection platform for proteases based on surface enhanced Raman scattering (SERS),” Biosens. Bioelectron. 65, 375–381 (2015).
[Crossref]

Xie, W.

A. Z. Subramanian, E. Ryckeboer, A. Dhakal, F. Peyskens, A. Malik, B. Kuyken, H. Zhao, S. Pathak, A. Ruocco, A. D. Groote, P. Wuytens, D. Martens, F. Leo, W. Xie, U. D. Dave, M. Muneeb, P. V. Dorpe, J. V. Campenhout, W. Bogaerts, P. Bienstman, N. L. Thomas, D. V. Thourhout, Z. Hens, G. Roelkens, and R. Baets, “Silicon and silicon nitride photonic circuits forspectroscopic sensing on-a-chip,” Photonics Res. 3(5), B47–B59 (2015).
[Crossref]

Xua, G.

L. Hu, S. Han, S. Parveen, Y. Yuan, L. Zhang, and G. Xua, “Highly sensitive fluorescent detection of trypsin based on BSA-stabilized gold nanoclusters,” Biosens. Bioelectron. 32(1), 297–299 (2012).
[Crossref]

Yang, K.-L.

I. L. H. Ong and K.-L. Yang, “Recent developments in protease activity assays and sensors,” Analyst 142(11), 1867–1881 (2017).
[Crossref]

Yang, Z.

Yuan, Y.

L. Hu, S. Han, S. Parveen, Y. Yuan, L. Zhang, and G. Xua, “Highly sensitive fluorescent detection of trypsin based on BSA-stabilized gold nanoclusters,” Biosens. Bioelectron. 32(1), 297–299 (2012).
[Crossref]

Zeng, H.

Zhang, D.

F. Wei, D. Zhang, N. J. Halas, and J. D. Hartgerink, “Aromatic Amino Acids Providing Characteristic Motifs in the Raman and SERS Spectroscopy of Peptides,” J. Phys. Chem. B 112(30), 9158–9164 (2008).
[Crossref]

Zhang, F.

Zhang, H.

Zhang, L.

L. Hu, S. Han, S. Parveen, Y. Yuan, L. Zhang, and G. Xua, “Highly sensitive fluorescent detection of trypsin based on BSA-stabilized gold nanoclusters,” Biosens. Bioelectron. 32(1), 297–299 (2012).
[Crossref]

Zhang, X.

C. Sun, K.-H. Su, J. Valentine, Y. T. Rosa-Bauza, J. A. Ellman, O. Elboudwarej, B. Mukherjee, C. S. Craik, M. A. Shuman, F. F. Chen, and X. Zhang, “Time-Resolved Single-Step Protease Activity Quantification Using Nanoplasmonic Resonator Sensors,” ACS Nano 4(2), 978–984 (2010).
[Crossref]

Zhao, B.

Zhao, H.

A. Z. Subramanian, E. Ryckeboer, A. Dhakal, F. Peyskens, A. Malik, B. Kuyken, H. Zhao, S. Pathak, A. Ruocco, A. D. Groote, P. Wuytens, D. Martens, F. Leo, W. Xie, U. D. Dave, M. Muneeb, P. V. Dorpe, J. V. Campenhout, W. Bogaerts, P. Bienstman, N. L. Thomas, D. V. Thourhout, Z. Hens, G. Roelkens, and R. Baets, “Silicon and silicon nitride photonic circuits forspectroscopic sensing on-a-chip,” Photonics Res. 3(5), B47–B59 (2015).
[Crossref]

Zhou, M.

Zhou, X.

Z. Wu, Y. Liu, Y. Liu, H. Xiao, A. Shen, X. Zhou, and J. Hu, “A simple and universal “turn-on” detection platform for proteases based on surface enhanced Raman scattering (SERS),” Biosens. Bioelectron. 65, 375–381 (2015).
[Crossref]

Z. Wu, Y. Liu, X. Zhou, A. Shen, and J. Hu, “A “turn-off” SERS-based detection platform for ultrasensitive detection of thrombin based on enzymatic assays,” Biosens. Bioelectron. 44, 10–15 (2013).
[Crossref]

Zhu, G.

G. Zhu, X. Zhu, Q. Fan, and X. Wan, “Raman spectra of amino acids and their aqueous solutions,” Spectrochim. Acta, Part A 78(3), 1187–1195 (2011).
[Crossref]

Zhu, X.

G. Zhu, X. Zhu, Q. Fan, and X. Wan, “Raman spectra of amino acids and their aqueous solutions,” Spectrochim. Acta, Part A 78(3), 1187–1195 (2011).
[Crossref]

ACS Appl. Mater. Interfaces (1)

A. N. Ramya, M. M. Joseph, J. B. Nair, V. Karunakaran, N. Narayanan, and K. K. Maiti, “New Insight of Tetraphenylethylene-based Raman Signatures for Targeted SERS Nanoprobe Construction Toward Prostate Cancer Cell Detection,” ACS Appl. Mater. Interfaces 8(16), 10220–10225 (2016).
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ACS Nano (1)

C. Sun, K.-H. Su, J. Valentine, Y. T. Rosa-Bauza, J. A. Ellman, O. Elboudwarej, B. Mukherjee, C. S. Craik, M. A. Shuman, F. F. Chen, and X. Zhang, “Time-Resolved Single-Step Protease Activity Quantification Using Nanoplasmonic Resonator Sensors,” ACS Nano 4(2), 978–984 (2010).
[Crossref]

ACS Photonics (2)

F. Peyskens, A. Dhakal, P. Van Dorpe, N. Le Thomas, and R. Baets, “Surface Enhanced Raman Spectroscopy Using a Single Mode Nanophotonic-Plasmonic Platform,” ACS Photonics 3(1), 102–108 (2016).
[Crossref]

A. Dhakal, C. Wuytens, F. Peyskens, K. Jans, N. Le Thomas, and R. Baets, “Nanophotonic waveguide enhanced Raman spectroscopy of biological submonolayers,” ACS Photonics 3(11), 2141–2149 (2016).
[Crossref]

Analyst (2)

I. L. H. Ong and K.-L. Yang, “Recent developments in protease activity assays and sensors,” Analyst 142(11), 1867–1881 (2017).
[Crossref]

K. Welser, R. Adsley, B. M. Moore, W. C. Chan, and J. W. Aylott, “Protease sensing with nanoparticle based platforms,” Analyst 136(1), 29–41 (2011).
[Crossref]

APL Photonics (1)

A. Raza, S. Clemmen, P. Wuytens, M. Muneeb, M. Van Daele, J. Dendooven, C. Detavernier, A. Skirtach, and R. Baets, “ALD assisted nanoplasmonic slot waveguide for on-chip Enhanced Raman Spectroscopy,” APL Photonics 3(11), 116105 (2018).
[Crossref]

Appl. Opt. (1)

Biol. Proced. Online (1)

H. P. Erickson, “Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy,” Biol. Proced. Online 11(1), 32–51 (2009).
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E. Gizem, M. Hedström, and B. Mattiasson, “A sensitive and real-time assay of trypsin by using molecular imprinting-based capacitive biosensor,” Biosens. Bioelectron. 86, 557–565 (2016).
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L. Hu, S. Han, S. Parveen, Y. Yuan, L. Zhang, and G. Xua, “Highly sensitive fluorescent detection of trypsin based on BSA-stabilized gold nanoclusters,” Biosens. Bioelectron. 32(1), 297–299 (2012).
[Crossref]

Z. Wu, Y. Liu, X. Zhou, A. Shen, and J. Hu, “A “turn-off” SERS-based detection platform for ultrasensitive detection of thrombin based on enzymatic assays,” Biosens. Bioelectron. 44, 10–15 (2013).
[Crossref]

Z. Wu, Y. Liu, Y. Liu, H. Xiao, A. Shen, X. Zhou, and J. Hu, “A simple and universal “turn-on” detection platform for proteases based on surface enhanced Raman scattering (SERS),” Biosens. Bioelectron. 65, 375–381 (2015).
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Chem. Rev. (1)

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Faraday Discuss. (1)

P. C. Wuytens, H. Demol, N. Turk, K. Gevaert, A. Skirtach, M. Lamkanfi, and R. Baets, “Gold nanodome SERS platform for label-free detection of protease activity,” Faraday Discuss. 205, 345–361 (2017).
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FASEB J. (1)

C. G. Smith and J. R. Vane, “The Discovery of Captopril,” FASEB J. 17(8), 788–789 (2003).
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J. Am. Chem. Soc. (1)

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J. Opt. Soc. Am. B (1)

J. Phys. Chem. B (1)

F. Wei, D. Zhang, N. J. Halas, and J. D. Hartgerink, “Aromatic Amino Acids Providing Characteristic Motifs in the Raman and SERS Spectroscopy of Peptides,” J. Phys. Chem. B 112(30), 9158–9164 (2008).
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J. Phys. Chem. C (1)

M. Tabatabaei, A. Sangar, N. Kazemi-Zanjani, P. Torchio, A. Merlen, and F. Lagugné-Labarthet, “Optical Properties of Silver and Gold Tetrahedral Nanopyramid Arrays Prepared by Nanosphere Lithography,” J. Phys. Chem. C 117(28), 14778–14786 (2013).
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J. Raman Spectrosc. (1)

C. L. Weeks, A. Polishchuk, Z. Getahun, W. F. DeGrado, and T. G. Spiro, “Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the νC≡N band of 4-cyanophenylalanine,” J. Raman Spectrosc. 39(11), 1606–1613 (2008).
[Crossref]

Mass Spectrom. Rev. (1)

E. Vandermarliere, M. Michael, and M. Lennart, “Getting intimate with trypsin, the leading protease in proteomics,” Mass Spectrom. Rev. 32(6), 453–465 (2013).
[Crossref]

Materials (1)

A. Dhakal, P. Wuytens, A. Raza, N. Le Thomas, and R. Baets, “Silicon Nitride Background in Nanophotonic Waveguide Enhanced Raman Spectroscopy,” Materials 10(2), 140 (2017).
[Crossref]

Nanomaterials (1)

N. Turk, A. Raza, P. Wuytens, H. Demol, M. Van Daele, C. Detavernier, A. Skirtach, K. Gevaert, and R. Baets, “Comparison of Free-Space and Waveguide-Based SERS Platforms,” Nanomaterials 9(10), 1401 (2019).
[Crossref]

Nanophotonics (1)

F. Peyskens, P. Wuytens, A. Raza, P. Van Dorpe, and R. Baets, “Waveguide excitation and collection of surface-enhanced Raman scattering from a single plasmonic antenna,” Nanophotonics 7(7), 1299–1306 (2018).
[Crossref]

Nanoscale (1)

L. Chen, X. Fu, and J. Li, “Ultrasensitive surface-enhanced Raman scattering detection of trypsin based on anti-aggregation of 4-mercaptopyridine-functionalized silver nanoparticles: an optical sensing platform toward proteases,” Nanoscale 5(13), 5905–5911 (2013).
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Opt. Express (8)

A. Raza, S. Clemmen, P. Wuytens, M. de Goede, A. S. K. Tong, N. Le Thomas, C. Liu, J. Suntivich, A. G. Skirtach, S. M. Garcia-Blanco, D. J. Blumenthal, J. S. Wilkinson, and R. Baets, “High index contrast photonic platforms for on-chip Raman spectroscopy,” Opt. Express 27(16), 23067–23079 (2019).
[Crossref]

A. Dhakal, A. Raza, F. Peyskens, A. Z. Subramanian, S. Clemmen, N. Le Thomas, and R. Baets, “Efficiency of evanescent excitation and collection of spontaneous Raman scattering near high index contrast channel waveguides,” Opt. Express 23(21), 27391–27404 (2015).
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E. P. Haglund, S. Kumari, P. Westbergh, J. S. Gustavsson, G. Roelkens, R. Baets, and A. Larsson, “Silicon-integrated short-wavelength hybrid-cavity VCSEL,” Opt. Express 23(26), 33634–33640 (2015).
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F. Tang, P.-M. Adam, and S. Boutami, “Theoretical investigation of SERS nanosensors based on hybrid waveguides made of metallic slots and dielectric strips,” Opt. Express 24(19), 21244–21255 (2016).
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X. Nie, E. Ryckeboer, G. Roelkens, and R. Baets, “CMOS-compatible broadband co-propagative stationary Fourier transform spectrometer integrated on a silicon nitride photonics platform,” Opt. Express 25(8), A409–A418 (2017).
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P. C. Wuytens, A. G. Skirtach, and R. Baets, “On-Chip Surface-Enhanced Raman Spectroscopy using Nanosphere-Lithography Patterned Antennas on Silicon Nitride Waveguides,” Opt. Express 25(11), 12926–12934 (2017).
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Q. Cao, J. Feng, H. Lu, H. Zhang, F. Zhang, and H. Zeng, “Surface-enhanced Raman scattering using nanoporous gold on suspended silicon nitride waveguides,” Opt. Express 26(19), 24614–24620 (2018).
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D. M. Kita, J. Michon, and J. Hu, “A packaged, fiber-coupled waveguide-enhanced Raman spectroscopic sensor,” Opt. Express 28(10), 14963–14972 (2020).
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Opt. Lett. (2)

Optica (1)

Photonics Res. (1)

A. Z. Subramanian, E. Ryckeboer, A. Dhakal, F. Peyskens, A. Malik, B. Kuyken, H. Zhao, S. Pathak, A. Ruocco, A. D. Groote, P. Wuytens, D. Martens, F. Leo, W. Xie, U. D. Dave, M. Muneeb, P. V. Dorpe, J. V. Campenhout, W. Bogaerts, P. Bienstman, N. L. Thomas, D. V. Thourhout, Z. Hens, G. Roelkens, and R. Baets, “Silicon and silicon nitride photonic circuits forspectroscopic sensing on-a-chip,” Photonics Res. 3(5), B47–B59 (2015).
[Crossref]

Phys. Rev. B (1)

H. M. K. Wong, M. K. Dezfouli, L. Sun, S. Hughes, and A. S. Helmy, “Nanoscale Plasmonic Slot Waveguides for Enhanced Raman Spectroscopy,” Phys. Rev. B 98(8), 085124 (2018).
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RSC Adv. (1)

Y. Lai, S. Sun, T. He, S. Schlücker, and Y. Wang, “Raman-encoded microbeads for spectral multiplexing with SERS detection,” RSC Adv. 5(18), 13762–13767 (2015).
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Spectrochim. Acta, Part A (1)

G. Zhu, X. Zhu, Q. Fan, and X. Wan, “Raman spectra of amino acids and their aqueous solutions,” Spectrochim. Acta, Part A 78(3), 1187–1195 (2011).
[Crossref]

Other (2)

I. M. Verhamme, S. E. Leonard, and R. C. Perkins, “Proteases: Pivot Points in Functional Proteomics,” in Functional Proteomics Methods and Protocols, 313–392 (Humana Press, New York, 2018).

E. Le Ru and P. Etchegoin, Principles of Surface-Enhanced Raman Spectroscopy, Elsevier Science (2008).

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Figures (13)

Fig. 1.
Fig. 1. (a) The concept of protease activity detection via peptide bond cleavage using SERS, where the SERS signal originates from the aromatic amino acids phenylalanine (F) and 4-cyano-phenylalanine (CN-F). The peptide forms a monolayer on the gold nanostructures and is then cleaved by a protease (here trypsin). As the cleaved-off part of the peptide diffuses away from the gold surface, the corresponding SERS peak intensity decreases. (b) Peptide substrate for trypsin, written with using the single-letter amino acid code. White letters represent the aromatic amino acids that provide SERS signals, namely phenylalanine (F) and the non-natural 4-cyano-phenylalanine (CN-F).
Fig. 2.
Fig. 2. (top) Gold nanodomes are free-space SERS substrate with an average gap size of 12 nm. (bottom) Waveguide-based nanoplasmonic slot waveguides have an average gap size of 43 nm.
Fig. 3.
Fig. 3. SERS spectra of the peptide before and after trypsin addition, recorded on gold nanodomes. Addition of trypsin results in a decrease in the intensity of the SERS peak of phenylalanine (F) at 1003 cm−1.
Fig. 4.
Fig. 4. F/CN-F peak intensity ratio for the trypsin cleavage experiments performed on gold nanodomes. The box plot shows that the F/CN-F peak intensity ratio decreases by 30% after trypsin addition. If no trypsin is added, or after the addition of inactive trypsin, there is no change in the F/CN-F peak intensity ratio.
Fig. 5.
Fig. 5. Raw SERS spectrum of the trypsin peptide substrate acquired on the nanoplasmonic slot waveguide. The silicon nitride peak at 2330 cm−1 indicates that the light is guided in the waveguide, whereas the other two peaks originate from the peptide itself. The background originates predominantly from the silicon nitride waveguide.
Fig. 6.
Fig. 6. An example of the F/CN-F peak intensity ratio plot as a function of time obtained on a reference nanoplasmonic slot waveguide. The vertical dashed line indicates the average value of the F/CN-F peak intensity.
Fig. 7.
Fig. 7. SERS spectra of the peptide before and after trypsin addition acquired on nanoplasmonic slot waveguide. The decrease in the F peak at 1003 cm−1 indicates trypsin-mediated cleavage of the peptide. Each spectrum shown in the graph is the average of 10 background-subtracted measurements. For better visualization, the spectra were smoothed with the simple moving average with the window size of 3.
Fig. 8.
Fig. 8. A box plot of F/CN-F peak intensities before and after trypsin addition recorded on nanoplasmonic slot waveguide. Individual measurements are presented as gray dots.
Fig. 9.
Fig. 9. RP-HPLC chromatogram of the intact peptide (trypsin substrate). The measured mass (in Da) along with the identified peptide fraction is written above each HPLC peak.
Fig. 10.
Fig. 10. RP-HPLC chromatogram of the trypsin-digested peptide. The measured mass (in Da) along with the identified peptide fraction is written above each HPLC peak.
Fig. 11.
Fig. 11. SERS spectra of the RP-HPLC separated peptides from a bulk trypsin cleavage experiment. The spectra are normalized on the CN-F maximum peak intensity for easier comparison and offset on the y axis. The horizontal vertical lines represent the zero of each spectrum. The two vertical lines represent the positions of the characteristic SERS peaks of the phenylalanine (F) and 4-cyano-phenylalanine (CN-F). After trypsin digestion, a complete disappearance of the SERS peak of phenylalanine F is evident, as expected.
Fig. 12.
Fig. 12. SERS spectra of the intact peptide (green) and of the cleavage solution after 1 h of incubating the peptide with trypsin (blue). The three spectra for each condition come from three different gold nanodome samples, all labelled under the same conditions. All spectra are normalized on the CN-F peak at 1180 cm−1.
Fig. 13.
Fig. 13. A box plot of F/CN-F peak intensities before (Ref) and after (Try) trypsin addition for the spectra shown in Fig. 12. Each box plot corresponds to one SERS spectrum in the previous figure.