Fluorescence resonance energy transfer (FRET) is one of the powerful tools used to study the dynamics of biomolecules.
By monitoring the energy transferred from a donor fluorophore to an acceptor fluorophore, one can determine the spatial
proximity between the fluorophores on the nanometer scale and thus extract information regarding interactions between
biomolecules. Here we demonstrate a novel way of measuring FRET from oligonucleotides using an integrated
optofluidic chip containing a planar liquid-core waveguide that can guide liquid and light simultaneously. FRET
experiments were carried out using fluorescein and Cy3 labeled oligonucleotides FRET pairs. An excitation laser was
fiber-coupled to a solid-core waveguide perpendicular to the chip's liquid-core channel. A FRET efficiency of 50% was
measured in good agreement with bulk microscopy experiments. By photobleaching the acceptors and manipulating the
fluidic flow, we also demonstrated controllable FRET events: an increase in donor signal, a decrease in acceptor signal
and the recovery of FRET due to the influx of new FRET pairs. The flexibility of our chip design also allows for
improvements such as separate donor and acceptor detection at either chip end using integrated filters.
Antiresonant reflecting optical waveguides (ARROWs) provide a promising approach to realizing high-sensitivity
sensing platforms on planar substrates. We have previously developed ARROW platforms that guide light in
hollow cores filled with liquid and gas media. These platforms include integrated traditional solid waveguides
to direct light into and out of sensing media. To improve the sensitivity of these platforms for optical sensing,
hollow waveguide loss must be reduced. We are working towards this by using anisotropic plasma etching to
create near-ideal hollow ARROW geometries. These structures rely on an etching mask that also serves as the
sacrificial core for the waveguide. This self-aligned process creates a hollow waveguide on a pedestal which is
surrounded by a terminal layer of air in three directions. We previously produced ARROWs by pre-etching the
silicon substrate and aligning the sacrificial core to the pedestal. However, this necessitates using a pedestal
which is wider than the core, leading to higher loss and poor reproducibility. We have also increased the hollow
to solid waveguide transmission efficiency by using a design that coats the sides and top of the hollow core with
a single layer of silicon dioxide. Using this design, we have demonstrated an interface transmission improvement
of more than two times. A much improved optical sensor platform will incorporate both of these features, using
the self-aligned pedestal process for most of the length of the hollow waveguides to decrease loss, and employing
the single layer design only at the interfaces to improve hollow-solid waveguide coupling.
We review our recent progress in bringing fluorescent correlation spectroscopy (FCS) of single molecules on a silicon
optofluidic platform. Starting from basic concepts and applications of FCS we move to a description of our integrated
optofluidic device, briefly outlining the physics behind its function and relevant geometrical characteristics. We then
derive an FCS theoretical model for our sensor geometry, which we subsequently apply to the examination of molecular
properties of single fluorophores and bioparticles. The model allows us to extract the diffusion coefficient, translational
velocity and local concentration of particles in question. We conclude with future directions of this research.
Previously, we created antiresonant reflecting optical waveguides (ARROWs) with hollow cores that guide light through
gas and liquid media. We have demonstrated that these ARROWs can be used in sensing applications with single
particle sensitivity using fluorescence correlation spectroscopy. To increase sensitivity for single molecule sensing, we
have improved our initial designs and fabrication methods to decrease ARROW background fluorescence and improve
transitions between solid and hollow waveguides. Photoluminescence of ARROW layers creates background
fluorescence that masks the desired fluorescence signals. To improve sensitivity, we have optimized the PECVD
ARROW layers to minimize the photoluminescence of each layer. Sensing applications require that hollow waveguides
interface with solid waveguides on the substrate to direct light into and out of test media. Our previous ARROW designs
required light at these interfaces to pass through the anti-resonant layers. Although in theory, high transmission through
ARROW layers can be achieved, in practice, passing through these layers has limited transmission efficiencies. A new
design coats the top and sides of the hollow core with only silicon dioxide, allowing light at interfaces to pass directly
from silicon dioxide into the hollow core. This new design exhibits good mode confinement in the hollow core.
We have previously produced antiresonant reflecting optical waveguides (ARROWs) with hollow cores that can guide
light through liquid or gas media. In order to utilize these structures in sophisticated sensing applications, we have
improved our initial designs and fabrication methods to increase yield, lower waveguide transmission loss, and
incorporate structural features into the waveguides themselves. Yields have been increased by optimizing PECVD film
conformality leading to greater sidewall strength for hollow waveguides. Sensing applications require interfacing hollow
waveguides with solid waveguides on the surface of a substrate to direct light on and off a chip and into and out of a test
medium. Previous interfaces required light transferring from solid to hollow waveguides to pass through the antiresonant
layers, with measured transmission efficiencies of about 30%. By removing the ARROW layers at the
interfaces, transmission efficiencies at these interfaces can be improved to greater than 95%. We also demonstrate the
fabrication of micropore structures on the hollow waveguides to be used for chemical sensing. A fabrication method has
been developed that allows for removal of the thick top oxide and nitride ARROW layers leaving only a thin nitride membrane directly over the hollow core allowing controlled access to test media.
The combination of integrated optics and microfluidics in planar optofluidic devices carries the potential for novel
compact and ultra-sensitive detection in liquid and gaseous media. Single molecule fluorescence detection sensitivity in
planar beam geometry was recently demonstrated in liquid-core antiresonant reflecting optical waveguides (ARROWs)
fabricated on a silicon chip. A key component of a fully integrated single-molecule sensor is the addition of an optical
filtering capability to separate excitation beams from much weaker generated fluorescence or scattering signals. This
capability will eventually allow for integration of the photodetector on the same chip as the optofluidic sensing part. It
has been theoretically shown that the wavelength-dependent transmission of liquid-core ARROWs can be tailored to
efficiently separate excitation and fluorescence. Here, we present the wavelength dependent transmission of air-core
ARROW waveguides, using a highly nonlinear photonic crystal fiber to generate a broadband excitation spectrum, and
the design of liquid-core ARROW waveguides with integrated filter function. The air-core waveguide loss shows
pronounced wavelength dependence in good agreement with the design, demonstrating the potential of tailoring the
optical properties of liquid-core waveguides to accommodate single-molecule sensing on a chip. We also present an
ARROW design to produce wavelength-dependent transmission that is optimized for fluorescence resonance energy
transfer (FRET) studies with high transmission at 573 nm and 668nm, and low transmission at 546 nm.
We discuss the development of novel integrated optical sensors with single molecule detection sensitivity. These sensors are based on liquid-core antiresonant reflecting optical waveguides (ARROWs) that allow for simultaneously guiding light and molecules in liquid solution through micron-sized channels on a chip. Using liquid-core ARROWs as the main building block, two-dimensional planar sensor arrays with sensitivity down to the single molecule level can be fabricated. We present the basic design principle for ARROW waveguides and methods to improve waveguide loss. The influence of surface roughness on the waveguide loss is described. We discuss highly efficient fluorescence detection in both one and two dimensional planar waveguide geometries. Avenues towards subsequent integration with microfluidic systems are presented.
We have developed a fabrication method for hollow anti-resonant reflecting waveguides (ARROW) on planar silicon substrates. Our fabrication technique is a bottom-up process making use of a sacrificial core material which is removed in an acid etch, leaving a hollow channel. This method is compatible with standard silicon processing steps, enabling the production of integrated devices. Using different core materials, we have build hollow ARROW waveguides with different core geometries, and have also demonstrated the fabrication of solid-core waveguides to interface with the hollow ARROWs. By optimizing the layer structure and fabrication process, we can reduce the optical loss of these waveguides to below 0.33/cm for liquid-filled waveguides and 2.4/cm for air-core waveguides.