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Research - Enhanced Fluorescence

Gene Expression Microarrays

The use of microarrays to determine gene expression levels from biological samples has become an extremely informative procedure for life sciences researchers.  These DNA microarrays promise to impact the practice of medicine, particularly in the diagnosis and treatment of cancer.  Currently, microarrays are performed on glass microscope slides and are capable of discerning large changes in gene expression between two biological tissues.  However, these microarrays are not capable of accurately determining smaller changes on the order of a few to dozens of nucleic acid molecules.  By using photonic crystals as the substrate to perform the microarray, we can take advantage of unique nanoscale optical effects to more strongly excite the fluorescent molecules used to tag the nucleic acid molecules.  Fluorescence from excited molecules can be further enhanced by altering the direction of emitted light to be more efficiently detected by the microarray instrumentation.  The result of this enhancement is an increase in the signal-to-noise ratio of the DNA microarray, which enables more accurate quantification of small changes in amounts of DNA present.  Because the photonic crystals we work with can be fabricated over large areas and easily integrated onto microscope slides, we can perform DNA microarray experiments with the same commercial microarray equipment used throughout many labs all over the world.  Currently we are collaborating with Professor Lila Vodkin of the Department of Crop Sciences here at UIUC to apply our photonic crystals to soybean genome microarray experiments in order to assess the performance of our photonic crystal substrate.

Financial Support: National Science Foundation and SRU Biosystems

Images of identical DNA microarray experiments performed on a glass slide and a photonic crystal.  Both microarrays have the same probe sequences and were exposed to the same soybean nucleic acid sample.  The photonic crystal enhanced fluorescence allows for detection of many sequences that cannot be detected on the glass slide.

Related Publications & Conference Presentations:

1. "Graded Wavelength One-Dimensional Photonic Crystal Reveals Spectral Characteristics of Enhanced Fluorescence," P.C. Mathias, N.Ganesh, W.Zhang, and B.T. Cunningham, Journal of Applied Physics, Vol. 103, No. 9, 2008.

2. "Enhanced fluorescence via photonic crystal slabs incorporating nanorod structures," W. Zhang, N. Ganesh, P.C. Mathias, and B.T. Cunningham, Conference on Lasers and Electro Optics, San Jose, CA, May 2008.

3. "Distance dependent amplification of molecular fluorescence via photonic crystal slabs," N. Ganesh, P.C. Mathias, W. Zhang, and B.T. Cunningham, Conference on Lasers and Electro Optics, San Jose, CA, May 2008.

4. "Distance dependence of fluorescence enhancement from photonic crystal surfaces," N. Ganesh, P.C. Mathias, W. Zhang, and B.T. Cunningham, Journal of Applied Physics, Vol. 103, p. 083104, 2008.

5. "Enhanced fluorescence emission from quantum dots on a photonic crystal surface," N. Ganesh, W. Zhang, P.C. Mathias and B.T. Cunningham, Nature Nanotechnology, Vol. 2, No. 8, p. 515-520, 2007.

6. "Combined Enhanced Fluorescence and Label-Free Biomolecular Sensing with a Two-Dimensional Photonic Crystal." P.C. Mathias, N.Ganesh, and B.T. Cunningham, IEEE LEOS Conference, Orlando, FL, October 2007.

7. "Photonic crystal enhanced fluorescence," N. Ganesh and B.T. Cunningham, 2007 CLEO/QELS Conference, Baltimore, MD, May 2007.

8. "Resonant enhancement of fluorescence from Quantum Dots on a Photonic Crystal Slab," N. Ganesh, W. Zhang, P.C. Mathias, and B.T. Cunningham, 2007 MRS Fall Meeting, San Francisco, CA, April 2007.

9. "Combined Enhanced Fluorescence and Label-Free Biomolecular Detection with a Photonic Crystal Surface," P.C. Mathias, N. Ganesh, Leo L. Chan, and B.T. Cunningham, Applied Optics, Vol. 26, No. 12, p. 2351-2360, 2007.