Combined microfluidic-optical DNA analysis with single-base-pair sizing capability.

DNA sequencing by microchip capillary electrophoresis (CE) enables cheap, high-speed analysis of low reagent volumes. One of its potential applications is the identification of genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant size range of 150-1000 base-pairs requires a variance of < 10.

Integrated mechano-optical hydrogen gas sensor using cantilever bending readout with a Si3N4 grated waveguide.

We demonstrate a proof of concept of a novel and compact integrated mechano-optical sensor for H(2) detection based on a microcantilever suspended above a Si(3)N(4) grated waveguide. The fabricated devices are mechanically and optically modeled and characterized. Sensing operation of the sensor is demonstrated with 1% H(2) in N(2).

Group-index and resonant field enhancement in a symmetric double-sided grated waveguide.

A numerical study has been carried out by means of the Green's function method to explore possible performance improvements of a simple grated waveguide (GWg) by the variations of its grated structure. It is shown that a GWg featuring symmetric two-sided grated structure of 16 teeth with a 60 nm groove depth and having a symmetric refractive index profile with a relatively large contrast between the grated and ungrated layers is capable of delivering largely improved device performance compared to that achieved previously with a one-sided grating of 40 nm groove depth and asymmetric index profile. The improvement is characterized by a remarkable 8-fold and 15-fold increase in the group index and the maximum field intensity, respectively, at the first resonance wavelength above the upper band edge (shorter wavelength), while relatively less improvement is found at the first resonance wavelength below the lower band edge (longer wavelength).

All-numerical noise filtering of fluorescence signals for achieving ultra-low limit of detection in biomedical applications.

We present an all-numerical method for post-processing of the fluorescent signal as obtained from labeled molecules by capillary electrophoresis (CE) in an optofluidic chip, on the basis of data filtering in the Fourier domain. It is shown that the method outperforms the well-known lock-in amplification during experiments in the reduction of noise by a factor of (square root)2. The method is illustrated using experimental data obtained during CE separation of molecules from a commercial DNA ladder with 17 fluorescently labeled molecules having different base-pair sizes.

Dual-point dual-wavelength fluorescence monitoring of DNA separation in a lab on a chip.

We present a simple approach in electrophoretic DNA separation and fluorescent monitoring that allows to identify the insertion or deletion of base-pairs in DNA probe molecules from genetic samples, and to perform intrinsic calibration/referencing for highly accurate DNA analysis. The principle is based on dual-point, dual-wavelength laser-induced fluorescence excitation using one or two excitation windows at the intersection of integrated waveguides and microfluidic channels in an optofluidic chip and a single, color-blind photodetector, resulting in a limit of detection of ~200 pM for single-end-labeled DNA molecules. The approach using a single excitation window is demonstrated experimentally, while the option exploiting two excitation windows is proposed theoretically.

Modulation-frequency encoded multi-color fluorescent DNA analysis in an optofluidic chip.

We introduce a principle of parallel optical processing to an optofluidic lab-on-a-chip. During electrophoretic separation, the ultra-low limit of detection achieved with our set-up allows us to record fluorescence from covalently end-labeled DNA molecules. Different sets of exclusively color-labeled DNA fragments-otherwise rendered indistinguishable by spatio-temporal coincidence-are traced back to their origin by modulation-frequency-encoded multi-wavelength laser excitation, fluorescence detection with a single ultrasensitive, albeit color-blind photomultiplier, and Fourier analysis decoding.

High-resolution electrophoretic separation and integrated-waveguide excitation of fluorescent DNA molecules in a lab on a chip.

By applying integrated-waveguide laser excitation to an optofluidic chip, fluorescently labeled DNA molecules of 12 or 17 different sizes are separated by CE with high operating speed and low sample consumption of approximately 600 pL. When detecting the fluorescence signals of migrating DNA molecules with a PMT, the LOD is as low as 2.1 pM.

Three-dimensional Mach-Zehnder interferometer in a microfluidic chip for spatially-resolved label-free detection.

Ultrafast laser writing of waveguides in glasses is a very flexible and simple method for direct on-chip integration of photonic devices. In this work we present a monolithic optofluidic device in fused silica providing label-free and spatially-resolved sensing in a microfluidic channel. A Mach-Zehnder interferometer is inscribed with the sensing arm orthogonally crossing the microfluidic channel and the reference arm passing over it.

Fluorescence monitoring of microchip capillary electrophoresis separation with monolithically integrated waveguides.

Using femtosecond laser writing, optical waveguides were monolithically integrated into a commercial microfluidic lab-on-a-chip device, with the waveguides intersecting a microfluidic channel. Continuous-wave laser excitation through these optical waveguides confines the excitation window to a width of 12 microm, enabling high-resolution monitoring of the passage of different types of fluorescent analytes when migrating and being separated in the microfluidic channel by microchip capillary electrophoresis. Furthermore, we demonstrate on-chip-integrated waveguide excitation and detection of a biologically relevant species, fluorescently labeled DNA molecules, during microchip capillary electrophoresis.

Optical sensing in microfluidic lab-on-a-chip by femtosecond-laser-written waveguides.

We use direct femtosecond laser writing to integrate optical waveguides into a commercial fused silica capillary electrophoresis chip. High-quality waveguides crossing the microfluidic channels are fabricated and used to optically address, with high spatial selectivity, their content. Fluorescence from the optically excited volume is efficiently collected at a 90 degree angle by a high numerical aperture fiber, resulting in a highly compact and portable device.

Theory for the measurements of dispersion characteristics in waveguiding structures with a scanning near-field optical microscope.

A theory is presented for the interpretation of scanning near-field optical microscope measurements on pulses propagating in waveguiding structures. It is shown how the dispersion characteristics of the propagating guided modes may be derived from such experiments. Then it is demonstrated how to calibrate the scanning tip position and to derive experimental values for reflection and transmission of modes in identical single-mode waveguides connected to a photonic device such as a micro cavity.