On-chip Optical DNA Sequencing via Integrated Waveguides
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Solution Overview
Problem
Current DNA sequencing methods face limitations in sequence read length, sensitivity, run time, and cost due to the need for labels and bulky optical tools, which restrict the length of accurate sequencing and increase costs.
Innovation Solution
The integration of a semiconductor chip with a laser and photodetectors on a single chip for real-time molecular sequencing, enabling both labeled and label-free techniques, which reduces costs and enhances sensitivity through optical field enhancement.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Illumination intensity
If labels are used for DNA sequencing, then signal strength is improved, but sequence read length is limited
Solution Approach 1:
The patent extracts and eliminates the label component from the sequencing system, achieving label-free DNA sequencing. This removes the fundamental limitation that caused signal fading over long sequences while maintaining detection capability through direct optical detection of nucleotide incorporation events.
Solution Approach 2:
The patent replaces the mechanical/chemical labeling system with a direct optical detection system. Instead of using fluorescent labels that fade, the system uses optical field enhancement and direct photodetection to observe nucleotide incorporation, substituting the labeling mechanism with a fundamentally different detection approach.
2Measurement precision
If multiple molecules are used to generate signals, then sensitivity is improved, but device complexity increases
Solution Approach 1:
The patent enables single molecules to generate detectable signals on their own through optical field enhancement. The enhanced optical fields amplify the signal from individual nucleotide incorporation events, eliminating the need to aggregate multiple molecules for detection while maintaining high sensitivity.
Solution Approach 2:
The patent changes the optical field parameters (intensity, confinement, resonance) to enhance the detection sensitivity. By optimizing the optical field characteristics in the nanoscale environment, the system achieves sufficient signal strength from single molecules without requiring multiple molecule aggregation.
3Measurement precision
If bulky optical tools are used for sequencing, then detection capability is improved, but cost increases
Solution Approach 1:
The patent merges the optical detection components directly into the sequencing device architecture. The photodetectors and optical field enhancement structures are integrated into the same nanoscale platform, eliminating the need for separate bulky optical tools and reducing overall system cost while maintaining detection capability.
Solution Approach 2:
The patent nests the detection functionality within the sequencing device structure itself. The photodetectors are positioned within or adjacent to the nanoscale sequencing environment, creating a compact nested architecture where the detection system is embedded in the sequencing platform rather than being a separate external instrument.
4Measurement precision
If pausing is implemented for signal acquisition, then measurement accuracy is improved, but run time increases
Solution Approach 1:
The patent enables continuous sequencing without pausing for signal acquisition. The optical field enhancement and direct detection system allow real-time monitoring of nucleotide incorporation events as they occur, eliminating the need to pause for signal acquisition while maintaining measurement accuracy through continuous optical detection.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach allows for cost-effective, high-sensitivity, and real-time DNA sequencing without the need for bulky equipment, improving sequence read length and reducing operational costs.
Implementation Method 1
a photodetector operably connected to the molecule trap, the photodetector to detect a spectral signature from a molecule in the molecule trap
Implementation Method 2
The laser is optically connected to the main waveguide
Implementation Method 3
providing a light source from a laser to the molecule trap via the waveguide
Data Source
AI summary
An integrated on-chip system and methods for real-time molecular sequencing. The system has a semiconductor chip and a laser. The semiconductor chip has integrated therein a main waveguide, a plurality of branch waveguides optically connected to the main waveguide, a plurality of nanochannels each having a fluid inlet and a fluid outlet, a plurality of molecule traps, a molecule trap at an intersection of a branch waveguide and a nanochannel, and a plurality of photodetectors operably connected to the plurality of molecule traps, one photodetector for a molecule trap, the photodetector to detect a spectral signature from a molecule in the molecule trap. The laser is optically connected to the main waveguide.