Photonic Crystal Surfaces for Label-Free Detection and Fluorescence Amplification

Summary

Principal Investigator: Brian T Cunningham
Affiliation: University of Illinois
Country: USA
Abstract: DNA microarrays are capable of simultaneously evaluating the relative expression levels of thousands of genes, and have developed rapidly since their initial introduction. As a result, DNA microarrays are now one of the most preferred technologies for identifying early biomarkers of toxicity and disease. The outcome of microarray studies can be affected by many technical and instrumental factors, resulting in major criticism regarding lack of reproducibility and accuracy of the derived data. Although fluorescent dyes, surface chemistries, spotting robots, hybridization chambers, detection instruments, and data analysis tools have all undergone substantial development and refinement, the microarray substrate itself remains as a simple glass surface. In this proposal, we describe how replacement of the glass surface with a special-purpose optical transducer can provide quality control information on the interspot and intraspot density of microarray spots that is currently completely lacking from microarray analysis, while simultaneously amplifying the intensity of fluorescent labels used to quantify hybridized DNA. By providing information on spot variability, (representing a major source of error in microarray analysis), while at the same time increasing the signal-to-noise ratio for detection of weakly expressed genes (where microarray platforms currently face a disadvantage compared to other quantitative gene expression platforms), the proposed project represents a fundamental advance in microarray technology. The optical transducer used to provide these features is a 2-dimensional photonic crystal (PC) surface that is designed to provide optical resonances that enable high resolution label-free imaging detection of deposited microarray spots and up to 550x enhanced detection sensitivity of commonly used microarray fluorescent dyes. The PC is fabricated by a large-area nanoreplica molding process on plastic substrates that are attached to standard glass microscope slides for compatibility with existing spotting robots, hybridization chambers, and detection instruments. Recently, large area PC surfaces have been developed by the Cunningham Group at Illinois as multifunctional optical transducers that can be designed to produce narrow-wavelength electromagnetic resonances at any desired wavelength, featuring high intensity fields that extend evanescently into the media on the PC surface. The interaction of the optical resonance with adsorbed biomolecules results in a highly localized shift of the resonant wavelength that is used to quantify the density of adsorbed material without the use of fluorescent labels, enabling label-free images of deposited DNA microarray spots to be measured with 4 5m spatial resolution over a PC comprising the entire surface of a conventional microarray slide. A PC surface may also be designed so that the optical resonance coincides with the wavelength of a laser used to excite a fluorescent dye, thereby increasing the fluorescent output intensity relative to the intensity that would occur on an ordinary glass microarray slide, using an effect called Enhanced Fluorescence (EF). The EF effect has been shown to result in ~50x increase in the detected fluorescence signal using commercially available microarray laser scanning instruments, but can be further enhanced when the PC is designed to also incorporate an optical resonance at the emission wavelength of the fluorophore, resulting in an additional 10x gain in sensitivity. In the proposed effort, we plan for the first time to apply 2-dimensional PC surfaces that incorporate optical resonances for both label-free detection and EF to spotted gene expression microarrays. The label-free resonance will be utilized to quantify the density variability of deposited DNA spots, thereby providing a quality- control tool that is not currently available to researchers using spotted arrays. The label-free images of DNA spots will be used to quantify interspot and intraspot density variability, providing information that will be used to eliminate defective spots from further analysis or as a means for normalizing the detected signal from subsequent fluorescent measurements. The EF resonance will be applied to enhance the output of Cy5- labeled hybridized DNA, enabling gene expression analysis to be conducted with lower sample concentrations and the ability to observe gene expression at lower levels than has previously been possible. The project will enable collaboration between faculty in Electrical Engineering, who developed the PC and EF technology under NSF funding, and faculty in Crop Science, who manage the NSF Soybean Functional Genomics Center, thus allowing the technology to be fully tested and developed for large arrays. The benefits of the method will be statistically quantified on a 7680-element gene array with sufficient inter-chip and intra- chip replicates and controls to quantify sensitivity and quality control gains obtained from each independent PC transducer function. The resulting capability will be broadly applicable across a wide range of scientific research that utilizes microarrays for human, animal, and plant gene expression analysis. Analysis of soybean gene arrays was selected as an ideal testbed for the new sensor technology, as it will not require the safety and approval protocols for working with human DNA and human-derived test samples. PUBLIC HEALTH RELEVANCE: The proposed project seeks to develop a technology platform for providing high- sensitivity label-free detection of biomolecules and substantial amplification of fluorescence output on large-area, plastic based nanostructured surfaces called "photonic crystals." The goal is to incorporate photonic crystal surfaces into DNA microarray slides to provide label-free quality control of array spots and the ability to more easily detect and identify genes with low expression levels. The project is relevant for the development of gene-based diagnostic tests that are accurate, reliable, and able to identify genes at low concentration.
Funding Period: ----------------2009 - ---------------2012-
more information: NIH RePORT

Top Publications

  1. pmc Multiplexed cancer biomarker detection using quartz-based photonic crystal surfaces
    Cheng Sheng Huang
    Department of Electrical and Computer Engineering, 1406 West Green Street, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, United States
    Anal Chem 84:1126-33. 2012
  2. doi Line-scanning detection instrument for photonic crystal enhanced fluorescence
    Vikram Chaudhery
    Department of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Opt Lett 37:2565-7. 2012
  3. doi Sensitive detection of protein and miRNA cancer biomarkers using silicon-based photonic crystals and a resonance coupling laser scanning platform
    Sherine George
    Department of Bioengineering, 1304 West Springfield Avenue, University of Illinois, Urbana Champaign, Illinois, 61801, USA
    Lab Chip 13:4053-64. 2013
  4. pmc A detection instrument for enhanced-fluorescence and label-free imaging on photonic crystal surfaces
    Ian D Block
    Dept of Electrical Engineering, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Opt Express 17:13222-35. 2009
  5. pmc Improved sensitivity of DNA microarrays using photonic crystal enhanced fluorescence
    Patrick C Mathias
    Department of Bioengineering, 1304 W Springfield Ave, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 82:6854-61. 2010
  6. pmc Photonic crystal enhanced fluorescence using a quartz substrate to reduce limits of detection
    Anusha Pokhriyal
    Dept of Physics, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Opt Express 18:24793-808. 2010
  7. pmc Application of photonic crystal enhanced fluorescence to cancer biomarker microarrays
    Cheng Sheng Huang
    Department of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 83:1425-30. 2011
  8. pmc Spatially selective photonic crystal enhanced fluorescence and application to background reduction for biomolecule detection assays
    Vikram Chaudhery
    Dept of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Opt Express 19:23327-40. 2011

Scientific Experts

  • Brian T Cunningham
  • Vikram Chaudhery
  • Cheng Sheng Huang
  • Meng Lu
  • Anusha Pokhriyal
  • Sherine George
  • James Polans
  • Ruimin Tan
  • Richard C Zangar
  • Patrick C Mathias
  • Lila O Vodkin
  • Nikhil Ganesh
  • Sarah I Jones
  • Ian D Block
  • Miki Takagi
  • NABIL AMRO
  • Yafang Tan
  • Placid Ferreira
  • Delkin O Gonzalez
  • Stephen Schulz
  • Hsin Yu Wu
  • German Bollero
  • Fuchyi Yang
  • Brian R Dorvel
  • Rashid Bashir

Detail Information

Publications9

  1. pmc Multiplexed cancer biomarker detection using quartz-based photonic crystal surfaces
    Cheng Sheng Huang
    Department of Electrical and Computer Engineering, 1406 West Green Street, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, United States
    Anal Chem 84:1126-33. 2012
    ..Using the PC resonance, biomarkers in mixed samples were detectable at the lowest concentrations tested (2.1-41 pg/mL), resulting in a three-log range of quantitative detection...
  2. doi Line-scanning detection instrument for photonic crystal enhanced fluorescence
    Vikram Chaudhery
    Department of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Opt Lett 37:2565-7. 2012
    ..The instrument provides a capability for sensitive and inexpensive analysis of cancer biomarkers in clinical applications...
  3. doi Sensitive detection of protein and miRNA cancer biomarkers using silicon-based photonic crystals and a resonance coupling laser scanning platform
    Sherine George
    Department of Bioengineering, 1304 West Springfield Avenue, University of Illinois, Urbana Champaign, Illinois, 61801, USA
    Lab Chip 13:4053-64. 2013
    ..Biomarkers were detected at concentrations as low as 0.1 pM. In a fluorescent microarray for detection of a breast cancer miRNA biomarker miR-21, the miRNA was detectable at a concentration of 0.6 pM. ..
  4. pmc A detection instrument for enhanced-fluorescence and label-free imaging on photonic crystal surfaces
    Ian D Block
    Dept of Electrical Engineering, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Opt Express 17:13222-35. 2009
    ....
  5. pmc Improved sensitivity of DNA microarrays using photonic crystal enhanced fluorescence
    Patrick C Mathias
    Department of Bioengineering, 1304 W Springfield Ave, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 82:6854-61. 2010
    ..This approach increases the dynamic range of a surface-bound fluorescence-based assay to reliably quantify small quantities of DNA that would be impossible with standard substrates...
  6. pmc Photonic crystal enhanced fluorescence using a quartz substrate to reduce limits of detection
    Anusha Pokhriyal
    Dept of Physics, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Opt Express 18:24793-808. 2010
    ..Using dose-response characterization of deposited fluorophore-tagged protein spots, the PCEF surface demonstrated a 140 × lower limit of detection compared to a conventional glass substrate...
  7. pmc Application of photonic crystal enhanced fluorescence to cancer biomarker microarrays
    Cheng Sheng Huang
    Department of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 83:1425-30. 2011
    ..Dose-response characterization of the photonic crystal antibody microarrays shows the capability to detect common cancer biomarkers in the <2 pg/mL concentration range within a mixed sample...
  8. pmc Spatially selective photonic crystal enhanced fluorescence and application to background reduction for biomolecule detection assays
    Vikram Chaudhery
    Dept of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Opt Express 19:23327-40. 2011
    ..Using the new approach, we demonstrate detection limits as low as 0.97 pg/ml for a representative protein biomarker in buffer...