Novel biosensors from photonic crystals

Screening the biochemical interaction of potential pharmaceutical compounds against a wide array of proteins and cells is a critical early step in drug discovery. In this way, costly failures can be avoided before the drug is introduced to animals and humans. Similarly, testing patients' blood or tissue samples for expression of a gene profile will become common practice in decisions regarding the most promising course of treatment. Reliable assays are also essential to applications such as environmental monitoring, crop protection, and the detection of biological warfare agents. Biological substances may be most simply sensed directly through their dielectric permittivity, a measure of how they affect electric fields, in so-called label-free detection. Even greater sensitivity may be obtained by attaching a fluorescent compound to the substance of interest, and then exciting the florescent molecule.

We have developed a new class of biosensors based on optical devices known as photonic crystals (PCs) that can be used for both label-free and fluorescence-based detection.^1–6 The key attributes for acceptance of new technology in these fields are sensitivity (how low a concentration of a chemical, protein, or gene may be detected), cost per test, and throughput (the number of tests that can be performed at once). PCs represent a unique and versatile class of optical devices for manipulating the electromagnetic fields associated with light. Through the proper application of PC design and fabrication, electromagnetic fields may be confined and concentrated to enhance the interaction between light and biological material in contact with the PC. We have developed methods that enable PC biosensors to be inexpensively produced in plastic, as well as associated instrumentation.⁷ Combined, the biosensors and detection instruments enable high-throughput detection of biochemical binding kinetics, imaging large arrays of biochemical tests,^8–11 and imaging detection of cells.^12–14

A PC biosensor consists of a periodic arrangement of dielectric (nonconducting) material in two or three dimensions (see Figure 1). If the periodicity and symmetry of the crystal and the dielectric constants of the materials used are chosen appropriately, the PC will selectively couple energy at particular wavelengths, while excluding others.¹⁵ A sensor structure consists of a low-refractive-index plastic material with a periodic surface structure that is coated with a thin layer of high-refractive-index dielectric material. Device structures based on linear gratings and 2D gratings have been demonstrated. The resonant wavelengths of a PC are easily measured by illuminating the surface with white light and collecting the reflected light from the sensor. The biosensor design enables a simple manufacturing process to produce sensor sheets in continuous rolls of plastic film that are hundreds of meters long.⁴ The mass production of a biosensor structure that is measurable in a noncontact mode over large areas enables the sensor to be incorporated into single-use disposable consumable items such as 96-, 384-, and 1536-well standard microplates and microarray slides, making the sensor compatible with the standard fluid handling infrastructure employed in most laboratories.

Figure 1. Device structure for the PC surface. (A) Schematic cross-section of the device structure. (B) Scanning electron microscope photo of top view and cross-section of a replica-molded 2D grating comprising an array of bumps coated with titanium dioxide (TiO₂) high-refractive-index dielectric material. (C) Photo of the fabricated device attached to an ordinary glass microscope slide, where the entire surface of the slide is populated by the PC sensor.

For label-free detection, the sensor operates by measuring changes in the wavelength of reflected light as biochemical binding events take place on the surface. For example, when DNA is deposited on the PC surface, an increase in the reflected wavelength occurs only where the mass density of the DNA results in a change in surface dielectric permittivity, and the amount of wavelength shift is proportional to the deposited mass density. The readout instrument is able to detect deposited mass changes on the surface with resolution less than 1pg/mm², and a spatial resolution of ∼4 μm per pixel (see Figure 2).⁷

Figure 2. Label-free detection of the adsorption of DNA on the PC surface by quantifying the shift in the resonantly reflected peak wavelength value (PWV). (A) Measurement of ∼2.5nm PWV shift due to the attachment of DNA to one location on the PC surface. (B) PWV shift image of a small section from a DNA microarray. Each DNA spot is ∼100μm in diameter.

For fluorescence biodetection, the PC period can be selected to provide a resonance for enhancing the laser excitation of fluorescent molecules near the PC surface. The periodicity allows for phase-matching of evanescent orders (decaying wavelengths) to localized leaky modes (where the wavelength decays in one direction) supported by the PC. Since the excited leaky modes are radiative but localized in space during their finite lifetimes, they can be engineered to have very high energy density within regions of the PC at resonance. The magnitude of this energy density is directly related to the resonant mode quality factor (or Q-factor), which in turn can be controlled by adjusting the parameters of the device. The intensity of emission of fluorescent samples that are absorptive at the resonant wavelengths can thus be greatly enhanced by placing them in proximity to regions where the resonant modes concentrate most of their energy. Using a 2D PC, excitation enhancement factors as great as 550(×) have been demonstrated (see Figure 3).¹⁶ At the same time, the existence of leaky modes that overlap the fluorescence emission spectrum opens up additional pathways for the emitted light to escape into free space. Besides direct emission, the fluorescence can couple to the overlapping leaky modes and (Bragg) scatter out of the structure, greatly reducing the amount of light trapped as guided modes (which are like leaky modes, but power is not lost to radiation as the electric field intensity decays), in comparison to an unpatterned substrate. The use of enhanced extraction has been demonstrated to provide an additional 13(×) enhancement of light collection from fluorescent quantum dots and will be experimentally demonstrated elsewhere.¹⁷

Figure 3. (A) Cross-section intensity images of 500μm-diameter spots of streptavidin-Cy5 compared without a PC, on the PC illuminated at an off-resonant angle, and on the PC measured at resonance: a 535× gain is demonstrated compared to the No-PC case. (B) Images of fluorescence intensity from 500μm-diameter spots of streptavidin-Cy5 on an unpatterned TiO₂ surface and an adjacent photonic crystal region on the same surface when the incident laser light matches the resonant condition.

In the context of a DNA gene expression array experiment, use of a PC surface instead of an ordinary glass slide will provide both quality control information on the density of deposited DNA microarray spots and a means for enhanced detection of hybridized DNA. The result should be more reliable characterization of genes that are weakly expressed. Improved fluorescence detection of proteins in patient-provided samples enables more accurate early detection of biomarkers that indicate the presence of specific medical conditions. Identifying individual cells or viral particles in a label-free fashion on a PC surface enables highly multiplexed but simple assays that are appropriate for characterizing the interaction of chemical compounds with live cells, and the development of tests for pathogens with low false alarm rates. Combining label-free and labeled modalities for the same substrate in environmental and homeland security detection applications provides additional means for discrimination and verification.