Abstract

We describe a recently developed oblique-incidence reflectivity difference (OI-RD) microscope, a form of polarization-modulated imaging ellipsometer, for label-free–high-throughput detection of biomolecular reactions on DNA and protein microarrays. We present examples of application of this technique to end-point and real-time investigations of DNA–DNA hybridization, antibody–antigen capture, and protein–small-molecule binding reactions. Compared to a conventional imaging ellipsometer based on the polarizer–compensator–sample–analyzer scheme and under the off-null condition, a polarization-modulated OI-RD microscope is inherently more sensitive by at least 1 order of magnitude to thickness changes on a solid surface. Compared with imaging surface plasmon resonance microscopes based on reflectance change on falling or rising slopes of the surface plasmon resonance, the OI-RD microscope (1) has a comparable sensitivity, (2) is applicable to conventional microscope glass slides, and (3) easily covers a field of view as large as the entire surface of a 1  in .×3  in . (2.54cm×7.62cm) microscope slide.

© 2007 Optical Society of America

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  1. M. Schena, Microarray Analysis (Wiley, 2003).
  2. H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
    [CrossRef] [PubMed]
  3. G. MacBeath, "Protein microarrays and proteomics," Nat. Genet. 32, 526-532 (2002).
    [CrossRef] [PubMed]
  4. T. Lindahl and R. D. Wood, "Quality control by DNA repair," Science 286, 1897-1905 (1999).
    [CrossRef] [PubMed]
  5. B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
    [CrossRef]
  6. J. S. Shumaker-Parry and C. T. Campbell, "Quantitative methods for spatially resolved adsorption/desorption measurements in real time by surface plasmon resonance microscopy," Anal. Chem. 76, 907-917 (2004).
    [CrossRef] [PubMed]
  7. L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
    [CrossRef]
  8. R. M. A. Azzam and N. M. Bashara, Ellipsometry and Polarized Light (Elsevier Science, 1987).
  9. G. Jin, R. Jansson, and H. Arwin, "Imaging ellipsometry revisited: development for visualization of thin transparent layers on silicon substrates," Rev. Sci. Instrum. 67, 2930-2936 (1996).
    [CrossRef]
  10. Z. H. Wang and G. Jin, "A label-free multi-sensing immuno-sensor based on imaging ellipsometry," Anal. Chem. 75, 6119-6123 (2003).
    [CrossRef] [PubMed]
  11. J. P. Landry, J. P. Gregg, and X. D. Zhu, "Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy," Opt. Lett. 29, 581-583 (2004).
    [CrossRef] [PubMed]
  12. J. Piehler, A. Brecht, and G. Gauglitz, "Affinity detection of low molecular weight analytes," Anal. Chem. 68, 139-143 (1996).
    [CrossRef] [PubMed]
  13. P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
    [CrossRef]
  14. Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
    [CrossRef]
  15. W. Schwarzacher, J. Gray, and X. D. Zhu, "Oblique incidence reflectivity difference as an in situ probe of electrodeposition: Co on Au," Electrochem. Solid-State Lett. 6, C73-C76 (2003).
    [CrossRef]
  16. X. D. Zhu, "Oblique-incidence optical reflectivity difference from a rough film of crystalline material," Phys. Rev. B 69, 115407 (2004).
    [CrossRef]
  17. J. P. Landry, J. Gray, M. K. O'Toole, and X. D. Zhu, "Incidence-angle dependence of optical reflectivity difference from an ultrathin film on solid surface," Opt. Lett. 31, 531-533 (2006).
    [CrossRef] [PubMed]
  18. B. Liedberg, C. Nylander, and I. Lundstrom, "Surface plasmon resonance for gas detection and biosensing," Sens. Actuators 4, 299-304 (1983).
    [CrossRef]
  19. X. D. Zhu, "Comparison of two optical techniques for label-free detection of biomolecular microarrays on solids," Opt. Commun. 259, 751-753 (2006).
    [CrossRef]
  20. W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
    [CrossRef] [PubMed]
  21. P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
    [CrossRef] [PubMed]

2006

X. D. Zhu, "Comparison of two optical techniques for label-free detection of biomolecular microarrays on solids," Opt. Commun. 259, 751-753 (2006).
[CrossRef]

J. P. Landry, J. Gray, M. K. O'Toole, and X. D. Zhu, "Incidence-angle dependence of optical reflectivity difference from an ultrathin film on solid surface," Opt. Lett. 31, 531-533 (2006).
[CrossRef] [PubMed]

2004

J. P. Landry, J. P. Gregg, and X. D. Zhu, "Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy," Opt. Lett. 29, 581-583 (2004).
[CrossRef] [PubMed]

X. D. Zhu, "Oblique-incidence optical reflectivity difference from a rough film of crystalline material," Phys. Rev. B 69, 115407 (2004).
[CrossRef]

J. S. Shumaker-Parry and C. T. Campbell, "Quantitative methods for spatially resolved adsorption/desorption measurements in real time by surface plasmon resonance microscopy," Anal. Chem. 76, 907-917 (2004).
[CrossRef] [PubMed]

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

2003

W. Schwarzacher, J. Gray, and X. D. Zhu, "Oblique incidence reflectivity difference as an in situ probe of electrodeposition: Co on Au," Electrochem. Solid-State Lett. 6, C73-C76 (2003).
[CrossRef]

Z. H. Wang and G. Jin, "A label-free multi-sensing immuno-sensor based on imaging ellipsometry," Anal. Chem. 75, 6119-6123 (2003).
[CrossRef] [PubMed]

2002

G. MacBeath, "Protein microarrays and proteomics," Nat. Genet. 32, 526-532 (2002).
[CrossRef] [PubMed]

2001

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

1999

T. Lindahl and R. D. Wood, "Quality control by DNA repair," Science 286, 1897-1905 (1999).
[CrossRef] [PubMed]

B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
[CrossRef]

1998

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

1996

G. Jin, R. Jansson, and H. Arwin, "Imaging ellipsometry revisited: development for visualization of thin transparent layers on silicon substrates," Rev. Sci. Instrum. 67, 2930-2936 (1996).
[CrossRef]

J. Piehler, A. Brecht, and G. Gauglitz, "Affinity detection of low molecular weight analytes," Anal. Chem. 68, 139-143 (1996).
[CrossRef] [PubMed]

1989

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
[CrossRef] [PubMed]

1983

B. Liedberg, C. Nylander, and I. Lundstrom, "Surface plasmon resonance for gas detection and biosensing," Sens. Actuators 4, 299-304 (1983).
[CrossRef]

Arwin, H.

G. Jin, R. Jansson, and H. Arwin, "Imaging ellipsometry revisited: development for visualization of thin transparent layers on silicon substrates," Rev. Sci. Instrum. 67, 2930-2936 (1996).
[CrossRef]

Azzam, R. M. A.

R. M. A. Azzam and N. M. Bashara, Ellipsometry and Polarized Light (Elsevier Science, 1987).

Bangham, R.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Bartelt, M. C.

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

Bashara, N. M.

R. M. A. Azzam and N. M. Bashara, Ellipsometry and Polarized Light (Elsevier Science, 1987).

Bertone, P.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Bidlingmaier, S.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Bilgin, M.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Brecht, A.

J. Piehler, A. Brecht, and G. Gauglitz, "Affinity detection of low molecular weight analytes," Anal. Chem. 68, 139-143 (1996).
[CrossRef] [PubMed]

Brockman, J. M.

B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
[CrossRef]

Campbell, C. T.

J. S. Shumaker-Parry and C. T. Campbell, "Quantitative methods for spatially resolved adsorption/desorption measurements in real time by surface plasmon resonance microscopy," Anal. Chem. 76, 907-917 (2004).
[CrossRef] [PubMed]

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

Casamayor, A.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Chen, Z. H.

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

Chinowsky, T. M.

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

Corn, R. M.

B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
[CrossRef]

Dean, R. A.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Fei, Y. Y.

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

Fong, C. Y.

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

Frutos, A. G.

B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
[CrossRef]

Gauglitz, G.

J. Piehler, A. Brecht, and G. Gauglitz, "Affinity detection of low molecular weight analytes," Anal. Chem. 68, 139-143 (1996).
[CrossRef] [PubMed]

Gerstein, M.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Gray, J.

J. P. Landry, J. Gray, M. K. O'Toole, and X. D. Zhu, "Incidence-angle dependence of optical reflectivity difference from an ultrathin film on solid surface," Opt. Lett. 31, 531-533 (2006).
[CrossRef] [PubMed]

W. Schwarzacher, J. Gray, and X. D. Zhu, "Oblique incidence reflectivity difference as an in situ probe of electrodeposition: Co on Au," Electrochem. Solid-State Lett. 6, C73-C76 (2003).
[CrossRef]

Gregg, J. P.

Hall, D.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Hendrickson, W. A.

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Jansen, R.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Jansson, R.

G. Jin, R. Jansson, and H. Arwin, "Imaging ellipsometry revisited: development for visualization of thin transparent layers on silicon substrates," Rev. Sci. Instrum. 67, 2930-2936 (1996).
[CrossRef]

Jin, G.

Z. H. Wang and G. Jin, "A label-free multi-sensing immuno-sensor based on imaging ellipsometry," Anal. Chem. 75, 6119-6123 (2003).
[CrossRef] [PubMed]

G. Jin, R. Jansson, and H. Arwin, "Imaging ellipsometry revisited: development for visualization of thin transparent layers on silicon substrates," Rev. Sci. Instrum. 67, 2930-2936 (1996).
[CrossRef]

Jung, L. S.

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

Lan, Ning

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Landry, J. P.

Liedberg, B.

B. Liedberg, C. Nylander, and I. Lundstrom, "Surface plasmon resonance for gas detection and biosensing," Sens. Actuators 4, 299-304 (1983).
[CrossRef]

Lindahl, T.

T. Lindahl and R. D. Wood, "Quality control by DNA repair," Science 286, 1897-1905 (1999).
[CrossRef] [PubMed]

Liu, H. B.

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

Liu, L. F.

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

Lundstrom, I.

B. Liedberg, C. Nylander, and I. Lundstrom, "Surface plasmon resonance for gas detection and biosensing," Sens. Actuators 4, 299-304 (1983).
[CrossRef]

MacBeath, G.

G. MacBeath, "Protein microarrays and proteomics," Nat. Genet. 32, 526-532 (2002).
[CrossRef] [PubMed]

Mar, M. N.

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

Merritt, E. A.

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Miller, P.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Mitchell, T.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Moufek, T.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Nabighian, E.

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

Nelson, B. P.

B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
[CrossRef]

Nylander, C.

B. Liedberg, C. Nylander, and I. Lundstrom, "Surface plasmon resonance for gas detection and biosensing," Sens. Actuators 4, 299-304 (1983).
[CrossRef]

Ohlendorf, D.

P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
[CrossRef] [PubMed]

O'Toole, M. K.

Paehler, A.

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Phizackerley, R. P.

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Piehler, J.

J. Piehler, A. Brecht, and G. Gauglitz, "Affinity detection of low molecular weight analytes," Anal. Chem. 68, 139-143 (1996).
[CrossRef] [PubMed]

Salemme, F.

P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
[CrossRef] [PubMed]

Satow, Y.

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Scheider, M.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Schena, M.

M. Schena, Microarray Analysis (Wiley, 2003).

Schwarzacher, W.

W. Schwarzacher, J. Gray, and X. D. Zhu, "Oblique incidence reflectivity difference as an in situ probe of electrodeposition: Co on Au," Electrochem. Solid-State Lett. 6, C73-C76 (2003).
[CrossRef]

Shumaker-Parry, J. S.

J. S. Shumaker-Parry and C. T. Campbell, "Quantitative methods for spatially resolved adsorption/desorption measurements in real time by surface plasmon resonance microscopy," Anal. Chem. 76, 907-917 (2004).
[CrossRef] [PubMed]

Smith, J. L.

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Thomas, P.

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

Wang, Z. H.

Z. H. Wang and G. Jin, "A label-free multi-sensing immuno-sensor based on imaging ellipsometry," Anal. Chem. 75, 6119-6123 (2003).
[CrossRef] [PubMed]

Weber, P.

P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
[CrossRef] [PubMed]

Wendoloski, J.

P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
[CrossRef] [PubMed]

Wood, R. D.

T. Lindahl and R. D. Wood, "Quality control by DNA repair," Science 286, 1897-1905 (1999).
[CrossRef] [PubMed]

Yang, G. Z.

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

Yee, S. S.

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

Zhu, H.

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Zhu, X. D.

X. D. Zhu, "Comparison of two optical techniques for label-free detection of biomolecular microarrays on solids," Opt. Commun. 259, 751-753 (2006).
[CrossRef]

J. P. Landry, J. Gray, M. K. O'Toole, and X. D. Zhu, "Incidence-angle dependence of optical reflectivity difference from an ultrathin film on solid surface," Opt. Lett. 31, 531-533 (2006).
[CrossRef] [PubMed]

X. D. Zhu, "Oblique-incidence optical reflectivity difference from a rough film of crystalline material," Phys. Rev. B 69, 115407 (2004).
[CrossRef]

J. P. Landry, J. P. Gregg, and X. D. Zhu, "Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy," Opt. Lett. 29, 581-583 (2004).
[CrossRef] [PubMed]

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

W. Schwarzacher, J. Gray, and X. D. Zhu, "Oblique incidence reflectivity difference as an in situ probe of electrodeposition: Co on Au," Electrochem. Solid-State Lett. 6, C73-C76 (2003).
[CrossRef]

Anal. Chem.

B. P. Nelson, A. G. Frutos, J. M. Brockman, and R. M. Corn, "Near-infrared surface plasmon resonance measurements of ultrathin films. 1. Angle shift and SPR imaging experiments," Anal. Chem. 71, 3928-2934 (1999).
[CrossRef]

J. S. Shumaker-Parry and C. T. Campbell, "Quantitative methods for spatially resolved adsorption/desorption measurements in real time by surface plasmon resonance microscopy," Anal. Chem. 76, 907-917 (2004).
[CrossRef] [PubMed]

Z. H. Wang and G. Jin, "A label-free multi-sensing immuno-sensor based on imaging ellipsometry," Anal. Chem. 75, 6119-6123 (2003).
[CrossRef] [PubMed]

J. Piehler, A. Brecht, and G. Gauglitz, "Affinity detection of low molecular weight analytes," Anal. Chem. 68, 139-143 (1996).
[CrossRef] [PubMed]

Appl. Phys. A

P. Thomas, E. Nabighian, M. C. Bartelt, C. Y. Fong, and X. D. Zhu, "An oblique-incidence optical reflectivity difference and LEED study of rare-gas growth on a lattice-mismatched metal substrate," Appl. Phys. A 79, 131-137 (2004).
[CrossRef]

Electrochem. Solid-State Lett.

W. Schwarzacher, J. Gray, and X. D. Zhu, "Oblique incidence reflectivity difference as an in situ probe of electrodeposition: Co on Au," Electrochem. Solid-State Lett. 6, C73-C76 (2003).
[CrossRef]

Langmuir

L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, "Quantitative interpretation of the response of surface plasmon resonance sensors to adsorbed films," Langmuir 14, 5636-5648 (1998).
[CrossRef]

Nat. Genet.

G. MacBeath, "Protein microarrays and proteomics," Nat. Genet. 32, 526-532 (2002).
[CrossRef] [PubMed]

Opt. Commun.

X. D. Zhu, "Comparison of two optical techniques for label-free detection of biomolecular microarrays on solids," Opt. Commun. 259, 751-753 (2006).
[CrossRef]

Opt. Lett.

Phys. Rev. B

X. D. Zhu, "Oblique-incidence optical reflectivity difference from a rough film of crystalline material," Phys. Rev. B 69, 115407 (2004).
[CrossRef]

Y. Y. Fei, X. D. Zhu, L. F. Liu, H. B. Liu, Z. H. Chen, and G. Z. Yang, "Oscillations in oblique-incidence optical reflection from a growth surface during layer-by-layer epitaxy," Phys. Rev. B 69, 233405 (2004).
[CrossRef]

Proc. Natl. Acad. Sci. USA

W. A. Hendrickson, A. Paehler, J. L. Smith, Y. Satow, E. A. Merritt, and R. P. Phizackerley, "Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation," Proc. Natl. Acad. Sci. USA 86, 2190-2194 (1989).
[CrossRef] [PubMed]

Rev. Sci. Instrum.

G. Jin, R. Jansson, and H. Arwin, "Imaging ellipsometry revisited: development for visualization of thin transparent layers on silicon substrates," Rev. Sci. Instrum. 67, 2930-2936 (1996).
[CrossRef]

Science

P. Weber, D. Ohlendorf, J. Wendoloski, and F. Salemme, "Structural origins of high-affinity biotin binding to streptavidin," Science 243, 85-88 (1989).
[CrossRef] [PubMed]

T. Lindahl and R. D. Wood, "Quality control by DNA repair," Science 286, 1897-1905 (1999).
[CrossRef] [PubMed]

H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, Ning Lan, R. Jansen, S. Bidlingmaier, T. Moufek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Scheider, "Global analysis of protein activities using proteome chips," Science 293, 2101-2105 (2001).
[CrossRef] [PubMed]

Sens. Actuators

B. Liedberg, C. Nylander, and I. Lundstrom, "Surface plasmon resonance for gas detection and biosensing," Sens. Actuators 4, 299-304 (1983).
[CrossRef]

Other

M. Schena, Microarray Analysis (Wiley, 2003).

R. M. A. Azzam and N. M. Bashara, Ellipsometry and Polarized Light (Elsevier Science, 1987).

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Figures (4)

Fig. 1
Fig. 1

OI-RD microscope for imaging biomolecular microarrays on a functionalized glass substrate. The substrate is on a translation stage that is movable along the x and y directions. PEM, photoelastic modulator for polarization modulation; PC, Pockel's cell for initial phase-shift adjustment; A, polarizing analyzer; PD, single-element or multielement photodetector.

Fig. 2
Fig. 2

OI-RD image of a 20 × 40 BSA microarray of one monolayer in thickness, obtained with a high-speed OI-RD microscope using a combination of line illumination and 152-element photodiode array detector. The contrast mechanism is Im { Δ p Δ s } . The contrast shown in the figure is on average what we have expected of a full BSA monolayer covering each of the 800 features. The pixel dimension of the image is 15 μ m × 15 μ m . There are 410 × 760 pixels in the image. The feature is 130 μ m in diameter, and the center-to-center separation between neighboring features is 300 μ m . The total scan time for this 800-feature image is 14 min. The N.A. of this microscope is 0.15.

Fig. 3
Fig. 3

(a) Image in Im { Δ p Δ s } of a 3 × 3 60-nt DNA microarray after reaction with a mixture of unlabeled DNA complementary to the first column and Cy5-labeled DNA complementary to the third column. Incidence angle θ inc is 45°. (b) Image in Im { Δ p Δ s } of a 4 × 4 antigen microarray after reaction with unlabeled goat anti-RB. θ inc is again 45°. (c) Image in Im { Δ p Δ s } of a 3 × 3 protein microarray after reaction with unlabeled streptavidin. θ inc in this case is 59°. The spatial resolution of the microscope that we used to obtain these images is 3 μ m .

Fig. 4
Fig. 4

Im { Δ p Δ s } from the interface between an epoxy-functionalized glass slide and the aqueous solution of BSA in 1 × PBS . At t = 0, the BSA is added to an initial 1 × PBS to make it a 7 .2   μ M BSA solution in less than 6 s. The saturated signal level at 0.008 corresponds to a full monolayer of BSA that covers 98% of the epoxy-functionalized surface. A magnetic stir is inside the fluid cell to continuously mix the solution during the experiment, ensuring a constant flux of BSA toward the glass surface.

Equations (123)

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1   in . × 3   in .
( 2.54 c m × 7.62 c m )
2 × 10 5
5   mm × 5   mm
r p / r s ρ tan   ψ   exp ( i δ )
Δ d
( Δ ψ ) 2
( Δ δ ) 2
( Δ d / λ ) 2
Δ ψ 0.01 °
Δ δ 0.01 °
0.0002
Δ ψ
Δ δ
Δ ψ 0.001 °
Δ δ 0.001 °
Δ δ 0.001 °
0.01   nm
r p 0 = | r p 0 |   exp ( i Φ p 0 )
r s 0 = | r s 0 |   exp ( i Φ s 0 )
r p = | r p |   exp ( i Φ p )
r s = | r s |   exp ( i Φ s )
Δ p = ( r p r p 0 ) / r p 0
Δ s = ( r s r s 0 ) / r s 0
Δ p Δ s
Re { Δ p Δ s } = ( | r p | | r p 0 | ) / | r p 0 | ( | r s | | r s 0 | ) / | r s 0 |
I m { Δ p Δ s } = ( Φ p Φ p 0 ) ( Φ s Φ s 0 )
ρ = r p / r s = tan   ψ   exp ( i δ )
Δ p Δ s ( ρ ρ 0 ) / ρ
{ Δ p Δ s } ( ψ ψ 0 ) / sin   ψ 0   cos   ψ 0 = Δ ψ / sin   ψ 0   cos   ψ 0
{ Δ p Δ s } = δ δ 0 = Δ δ
Δ p Δ s
Δ p Δ s i [ 4 π ε s ( tan   θ inc ) 2   cos   θ inc ε 0 1 / 2 ( ε s ε 0 ) ( ε s / ε 0 ( tan   θ inc ) 2 ) ] × ( ε d ε s ) ( ε d ε 0 ) Θ ε d ( d λ ) ,
θ inc
ε 0
ε d
ε s
ε d
ε d
Δ p Δ s
θ inc
θ inc
θ B
( ε 0
ε s
ε d
{ Δ p Δ s }
δ θ SPR ( 3 π d / λ ) ( ε d ε 0 ) / ε d
θ B
Δ p Δ s
Δ p Δ s
ε 0 = 1
ε s = 2.31
2.4 μ m
1 / e 2
1.7 μ m
Δ p Δ s
Δ p Δ s
15 μ m
300 μ m
150 μ m
500 μ m
0.1   Å
{ Δ p Δ s }
3 × 3
120 μ m
1.5 × 10 3
60 %
( Θ = 0.6 )
1.5 × 10 3
{ Δ p Δ s }
4 × 4
150 μ m
100 μ m
{ Δ p Δ s } ( 4 × 10 3 )
( Θ = 0.2 )
{ Δ p Δ s }
3 × 3
150 μ m
5   nm
ρ d = 1.35 g / cm 3
4.0 × 10 12 molecules / cm 2
4 ng / mm 2
λ = 532   nm
ε d
[ n d
{ Δ p Δ s } ( 1.7 × 10 2 )
1.4 × 10 12
molecules / cm 2
Θ = 0.35
ε d = 2.51
1 ×
1 × PBS
7.2 μ M
( 1.0 mg / ml )
{ Δ p Δ s }
t = 0
1 × PBS
1 × PBS
{ Δ p Δ s }
1.4   nm
ε d ( BSA ) = 2.5
n d ( BSA ) = 1.58
20 × 40
{ Δ p Δ s }
15 μ m × 15 μ m
410 × 760
130 μ m
300 μ m
{ Δ p Δ s }
3 × 3
θ inc
{ Δ p Δ s }
4 × 4
θ inc
{ Δ p Δ s }
3 × 3
θ inc
3 μ m
{ Δ p Δ s }
1 × PBS
1 × PBS
7 .2   μ M

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