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DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant range of 150-1000 base-pairs requires a sizing accuracy of S < 10^-3, while only S < 10^-2 were reported. Here we demonstrate a sizing accuracy of S = 4 x 10^-4, thereby paving the way for the envisaged applications.

Applying capillary electrophoresis, we separate and detect two sets of fluorescent-labeled DNA molecules in the 150-1000 base-pair range and achieve a sizing accuracy of 4x10^-4, enabling micro-chip analysis of single-base-pair deletion/insertion.

Direct femtosecond laser writing is used to integrate optical waveguides that intersect the microfluidic channels in a commercial optofluidic chip. With laser excitation, fluorescently labeled DNA molecules of different sizes are separated by capillary electrophoresis with high operating speed and low sample consumption (~ 600 pl). ...

We introduce a principle of parallel optical processing: modulation-frequency-encoded multi-wavelength laser excitation, fluorescence detection with a single detector, and Fourier analysis decoding. As an example, we demonstrate simultaneous detection of DNA fragments from different origins.

Use of optical principles for the detection and analysis of biomolecules and biotissue has a long-standing tradition, and highly sensitive optical methods have been developed. Integration on a microchip offers cost reduction and instrument miniaturization, thus enabling novel applications, but also allows reduced biosample volumes, higher sensitivity, and faster acquisition times. We demonstrate optical sensing with Bragg-grating cavities inscribed into optical waveguides for label-free sensing of antibody-antigen protein reactions and H2 gas sensing by stress-induced Pd-receptor microcantilever deflections. Furthermore, we introduce the method of modulation-frequency-encoded multi-wavelength fluorescent DNA analysis in an optofluidic chip during capillary electrophoresis separation, enabling detection down to the single-molecule level and allowing simultaneous analysis of DNA fragments from independent human genomic segments, associated with genetic predispositions to breast cancer and anemia, in a single experiment. Finally, by integrating wavelength-selective arrayed-waveguide gratings on a microchip, we demonstrate on-chip Raman spectroscopy and spectral-domain optical coherence tomography of biotissue.

Modulation-frequency-encoded fluorescence excitation enables the identification of end-labeled DNA samples of different genetic origin during their electrophoretic separation, opening perspectives for intrinsic size calibration, malign / healthy sample comparison, and exploitation of multiplex ligation-dependent probe amplification.

We present recent progress in the field of sensing fluorescently labeled biomolecules, as separated by micro-chip capillary electrophoresis, being a method to improve the detection limit of the fluorescence signal by numerical post-processing and a way for parallel detection of differently labeled sets of molecules using en-coded excitation.

Femtosecond-laser-written integrated waveguides enable multi-wavelength fluorescence sensing of flowing biomolecules in an optofluidic chip. Fluorescence from differently labeled biomolecules with distinct absorption wavelengths, encoded by uniquely modulating each excitation beam, is detected by a color-blind photodetector, and the origin of each signal is unraveled by Fourier analysis.

Electrophoretic separation of fluorescently labeled DNA molecules in on-chip microfluidic channels was monitored by integrated waveguide arrays, with simultaneous spatial and wavelength resolution. This is an important step toward point-of-care diagnostics with multiplexed DNA assays.

Monolithic integration of optical waveguides in a commercial lab-on-a-chip by femtosecond-laser material processing enables arbitrary 3D geometries of optical sensing structures in combination with fluidic microchannels. Integrated fluorescence monitoring of molecular separation, as applicable in point-of-care diagnostic bioassays is demonstrated.

We report on monolithic optical sensor integration in a lab-on-a-chip toward onchip diagnosis of all kinds of genetic diseases, e.g. breast cancer. Such an analysis of genetic diseases is based on the capillary electrophoresis separation of DNA fragments amplified from diagnostically relevant regions of the concerned gene. This paper presents a proof of principle, demonstrating real time integrated fluorescence monitoring during the capillary electrophoresis separation of fluorescent dyes as well as fluorescently labeled DNA molecules in an on-chip microfluidic channel. To this end, sensing waveguides were integrated monolithically by means of femtosecond laser irradiation, in a commercial fused silica lab-on-a-chip, to perpendicularly intersect the microfluidic separation channel. Laser excitation through these waveguides induces fluorescence in the flowing microfluidic plugs. Depending on the number of species present, and the difference between their mobility, a corresponding number of electropherogram peaks are detected. Detection has been performed by a CCD camera in order to visualize the on-chip events and to provide access to spatial information, as well as by a photomultiplier tube in order to detect low values of fluorescence signal. The present limit of detection is estimated to be approximately 6 nM. The presented setup achieves high spatial resolution due to the small cross section of the waveguides, ~12 μm. This is an improvement over the conventional approach to place a pinhole in the path of the fluorescence output signal generated by a broadband background illumination, e.g. with an Hg or a Xe lamp. Future work will focus on extension of this principle to real world diagnostic samples for development of a fast and compact point of care optical biosensing device. During the conference we will present the latest results in wavelengthmultiplexed fluorescence monitoring of DNA separation at low limits of detection.

Capillary electrophoresis separation in an on-chip integrated microfluidic channel is typically monitored with bulky, bench-top optical excitation/detection instrumentation. Optical waveguides allow confinement and transport of light in the chip directing it to a small volume of the microfluidic channel and collecting the emitted/transmitted radiation. However, the fabrication of optical waveguides or more complex photonic components integrated with the microfluidic channels is not a straightforward process, since it requires a localized increase of the refractive index of the substrate. Recently, a novel technique has emerged for the direct writing of waveguides and photonic circuits in transparent glass substrates by focused femtosecond laser pulses. In this work we demonstrate the integration of femtosecond laser written optical waveguides into a commercial microfluidic chip. We fabricate high quality waveguides intersecting the microchannels at arbitrary positions and use them to optically address with high spatial selectivity their content. In particular, we apply our technique to integrate optical detection in microchip capillary electrophoresis. Waveguides are inscribed at the end of the separation channel in order to optically excite the different plugs reaching that point; fluorescence from the labelled biomolecules crossing the waveguide output is efficiently collected at a 90° angle by a high numerical aperture optical fiber. The sensitivity of the integrated optical detection system was first evaluated filling the chip with a dye solution, obtaining a minimum detectable concentration of 40 pM. After dynamic coating of the microchannels with an EPDMA polymer we demonstrate electrophoresis of an oligonucleotide plug with concentration down to 1 nM and wavelength-selective monitoring of on-chip separation of three fluorescent dyes. Work is in progress on separation and detection of fluorescent-labeled DNA fragments, targeting specific, diagnostically relevant regions of a template DNA, for application to the detection of chromosome aberrations.

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 um, 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. We demonstrate on-chip-integrated waveguide excitation and detection of a biologically relevant species, fluorescently labeled Deoxyribonucleic acid (DNA) molecules, as well as separation of different dyes, Rhodamine-6G and Rhodamine-B during microchip capillary electrophoresis. Well-controlled plug formation as required for on-chip integrated capillary electrophoresis separation of DNA molecules, and the combination of waveguide excitation and a low detection limit will enable monitoring of extremely small quantities with high spatial resolution.

Femtosecond-laser-written optical waveguides were monolithically integrated into a commercial lab-on-a-chip to intersect a microfluidic channel. Laser excitation through these waveguides confines the excitation window to a width of 12 μm, enabling high-spatial-resolution monitoring of different fluorescent analytes, during their migration/separation in the microfluidic channel by capillary electrophoresis. Wavelength-selective monitoring of the on-chip separation of fluorescent dyes is implemented as a proof-of-principle. We envision well-controlled microfluidic plug formation, waveguide excitation, and a low limit of detection to enable monitoring of extremely small quantities with high spatial resolution.

This paper describes results obtained with a lab-on-a-chip with monolithically integrated optical waveguides. The waveguides are written with femtosecond laser pulses, enabling one to define location and dimensions of very confined detection windows along a microfluidic channel. The present results demonstrate the monitoring of plug passage of fluorescently labelled DNA molecules, during the process of microchip capillary electrophoresis.

Optical waveguides have been fabricated focusing femtosecond laser pulses into a commercial microfluidic chip. The waveguides intersect the channels and are used to optically excite their content. Fluorescence from the optically addressed volume is efficiently collected by a fiber, resulting in an highly compact and portable setup.

Fluorescence detection is known to be one of the most sensitive among the different optical sensing techniques. This work focuses on excitation and detection of fluorescence emitted by DNA strands labeled with fluorescent dye molecules that can be excited at a specific wavelength. Excitation occurs via optical channel waveguides written with femtosecond laser pulses applied coplanar with a microfluidic channel on a glass chip. The waveguides are optically characterized in order to facilitate the design of sensing structures which can be applied for monitoring the spatial separation of biochemical species as a result of capillary electrophoresis.

An overview is presented of research projects on optical sensing, in the Integrated Optical MicroSystems group of the MESA+ Institute for Nanotechnology at the University of Twente.