Optofluidic bioanalysis: fundamentals and applications.

Over the past decade, optofluidics has established itself as a new and dynamic research field for exciting developments at the interface of photonics, microfluidics, and the life sciences. The strong desire for developing miniaturized bioanalytic devices and instruments, in particular, has led to novel and powerful approaches to integrating optical elements and biological fluids on the same chip-scale system. Here, we review the state-of-the-art in optofluidic research with emphasis on applications in bioanalysis and a focus on waveguide-based approaches that represent the most advanced level of integration between optics and fluidics. We discuss recent work in photonically reconfigurable devices and various application areas. We show how optofluidic approaches have been pushing the performance limits in bioanalysis, e.g. in terms of sensitivity and portability, satisfying many of the key requirements for point-of-care devices. This illustrates how the requirements for bianalysis instruments are increasingly being met by the symbiotic integration of novel photonic capabilities in a miniaturized system.

Scalable Spatial-Spectral Multiplexing of Single-Virus Detection Using Multimode Interference Waveguides.

Simultaneous detection of multiple pathogens and samples (multiplexing) is one of the key requirements for diagnostic tests in order to enable fast, accurate and differentiated diagnoses. Here, we introduce a novel, highly scalable, photonic approach to multiplex analysis with single virus sensitivity. A solid-core multimode interference (MMI) waveguide crosses multiple fluidic waveguide channels on an optofluidic chip to create multi-spot excitation patterns that depend on both the wavelength and location of the channel along the length of the MMI waveguide. In this way, joint spectral and spatial multiplexing is implemented that encodes both spatial and spectral information in the time dependent fluorescence signal. We demonstrate this principle by using two excitation wavelengths and three fluidic channels to implement a 6x multiplex assay with single virus sensitivity. High fidelity detection and identification of six different viruses from a standard influenza panel is reported. This multimodal multiplexing strategy scales favorably to large numbers of targets or large numbers of clinical samples. Further, since single particles are detected unbound in flow, the technique can be broadly applied to direct detection of any fluorescent target, including nucleic acids and proteins.

Signal-to-noise Enhancement in Optical Detection of Single Viruses with Multi-spot Excitation.

We present fluorescence detection of single H1N1 viruses with enhanced signal to noise ratio (SNR) achieved by multi-spot excitation in liquid-core anti-resonant reflecting optical waveguides (ARROWs). Solid-core Y-splitting ARROW waveguides are fabricated orthogonal to the liquid-core section of the chip, creating multiple excitation spots for the analyte. We derive expressions for the SNR increase after signal processing, and analyze its dependence on signal levels and spot number. Very good agreement between theoretical calculations and experimental results is found. SNR enhancements up to 5x104 are demonstrated.

Improved environmental stability for plasma enhanced chemical vapor deposition SiO2 waveguides using buried channel designs.

Ridge and buried channel waveguides (BCWs) made using plasma-enhanced chemical vapor deposition SiO2 were fabricated and tested after being subjected to long 85°C water baths. The water bath was used to investigate the effects of any water absorption in the ridge and BCWs. Optical mode spreading and power throughput were measured over a period of three weeks. The ridge waveguides quickly absorbed water within the critical guiding portion of the waveguide. This caused a nonuniformity in the refractive index profile, leading to poor modal confinement after only seven days. The BCWs possessed a low index top cladding layer of SiO2, which caused an increase in the longevity of the waveguides, and after 21 days, the BCW samples still maintained ~20% throughput, much higher than the ridge waveguides, which had a throughput under 5%.

Spectrally reconfigurable integrated multi-spot particle trap.

Optical manipulation of small particles in the form of trapping, pushing, or sorting has developed into a vast field with applications in the life sciences, biophysics, and atomic physics. Recently, there has been increasing effort toward integration of particle manipulation techniques with integrated photonic structures on self-contained optofluidic chips. Here, we use the wavelength dependence of multi-spot pattern formation in multimode interference (MMI) waveguides to create a new type of reconfigurable, integrated optical particle trap. Interfering lateral MMI modes create multiple trapping spots in an intersecting fluidic channel. The number of trapping spots can be dynamically controlled by altering the trapping wavelength. This novel, spectral reconfigurability is utilized to deterministically move single and multiple particles between different trapping locations along the channel. This fully integrated multi-particle trap can form the basis of high throughput biophotonic assays on a chip.

Optofluidic wavelength division multiplexing for single-virus detection.

Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context--the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine.

Electro-optical detection of single λ-DNA.

Single λ-DNA molecules are detected on a nanopore-gated optofluidic chip electrically and optically. Statistical variations in the single particle trajectories are used to predict the intensity distribution of the fluorescence signals.

Dual-core optofluidic chip for independent particle detection and tunable spectral filtering.

We present the first integration of fluidically tunable filters with a separate particle detection channel on a single planar, optofluidic chip. Two optically connected, but fluidically isolated liquid-core antiresonant reflecting optical waveguide (ARROW) segments serve as analyte and spectral filter sections, respectively. Ultrasensitive detection of fluorescent nanobeads with high signal-to-noise ratio provided by a fluidically tuned excitation notch filter is demonstrated. In addition, reconfigurable filter response is demonstrated using both core index tuning and bulk liquid tuning. Notch filters with 43 dB rejection ratio and a record 90 nm tuning range are implemented by using different mixtures of ethylene glycol and water in the filter section. Moreover, absorber dyes and liquids with pH-dependent transmission in the filter channel provide additional spectral control independent of the waveguide response. Using both core index and pH control, independent filter tuning at multiple wavelengths is demonstrated for the first time. This extensive on-chip control over spectral filtering as one of the fundamental components of optical particle detection techniques offers significant advantages in terms of compactness, cost, and simplicity, and opens new opportunities for waveguide-based optofluidic analysis systems.

Tailoring the spectral response of liquid waveguide diagnostic platforms.

Liquid filled waveguides that form the basis for on-chip biophotonics diagnostic platforms have primarily found application in fluorescence and Raman spectroscopy experiments that require sensitive discrimination between weak analyte signals and a variety of background signals. Primary sources of background signal can include light from excitation sources (strong, narrow frequency band) and photoluminescence generated in waveguide cladding layers (weak, wide frequency band). Here we review both solid and liquid core filtering structures which are based on anti-resonant reflection that can be integrated with waveguides for attenuating undesirable optical bands. Important criteria to consider for an optimized biosensor include cladding layer materials that minimize broad-spectrum photoluminescence and optimize layer thicknesses for creating a desired spectral response in both solid and liquid guiding layers, and a microfabrication process capable of producing regions with variable spectral response. New results describing how spurious fluorescence can be minimized by optimized thermal growth conditions and how liquid-core filter discrimination can be tuned with liquid core waveguide length are presented.