Pacific Biosciences of California, Inc.

Shang Wang

Paul M Lundquist

Stephen Wilson Turner

Mark E McDonald

Annette Claire Grot

Aaron J Rulison

Hans Callebaut

Mathieu Foquet

Ariel Herrmann

Tsuei-Lian Wang

Deborah Pao-Tung Kwo

Mark Mcdonald

Integrated target waveguide devices and optical analytical systems comprising such devices are provided. The target devices include an optical coupler that is optically coupled to an integrated waveguide and that is configured to receive optical input from an optical source through free space, particularly through a low numerical aperture interface. The devices and systems are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices provide for the efficient and reliable coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.

Integrated target waveguide devices and systems for optical coupling

Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.

Illumination of optical analytical devices

We describe methods of producing gratings such as Bragg gratings with optical waveguides. Described are the writing and erasing of gratings within SiON waveguides by forming standing waves. Methods, systems, instruments, and devices are described that provide improved transmission of light through such waveguides.

Producing bragg gratings in optical waveguides

Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include optical waveguides for illumination of the optical reactions. In some embodiments, the devices comprise an optical waveguide comprising a plurality of optical cores and a cladding, a plurality of nanometer-scale apertures disposed on a surface of the device above the optical waveguide, such that optical energy passing through the plurality of optical cores of the optical waveguide illuminates the plurality of nanometer-scale apertures by an evanescent field that emanates from the waveguide, and a plurality of detectors optically coupled to the plurality of nanometer-scale apertures. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.

We have seen that some waveguides exhibit variable and increasing back reflection of single wavelength illumination over time, limiting their effectiveness and reliability. We have developed approaches to improve the transmission of these waveguides. We have found that by modulating the illumination wavelength over a small wavelength range we can reduce or eliminate this back reflection from the waveguide. In addition, we describe the writing and erasing of gratings within SiON waveguides by forming standing waves. Methods, systems, instruments, and devices are described that provide improved transmission of light through such waveguides.

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San Carlos, CA, United States of America

Shang Wang