Chamber-Free Nanosensor Sequencing Correcting Phase Errors
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Solution Overview
Problem
Current DNA sequencing technologies are cumbersome, expensive, and have limited throughput, with single-use disposables increasing costs and limiting complexity, and existing methods for clonal DNA sequencing suffer from phase errors leading to short read lengths.
Innovation Solution
The development of systems and methods for sequencing polynucleotides using chamber-free devices and nanosensors that allow for clonal or parallel sequencing, correcting phase errors through nucleotide combinations, chain terminating nucleotides, and oligonucleotide clamps, and employing reusable devices for improved engineering and cost-effectiveness.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If single-use disposable sensors and sequencing flow cells are used, then manufacturing complexity is reduced, but cost increases substantially
Solution Approach 1:
The patent applies disposable emulsion droplets as reaction containers instead of expensive reusable sensors. Each droplet is inexpensive to produce and used once for sequencing, eliminating the need for complex reusable sensor manufacturing while keeping per-reaction costs low through high-throughput parallel processing in millions of droplets
Solution Approach 2:
The sequencing system segments the reaction into millions of parallel emulsion droplets, each containing a single template molecule and polymerase complex. This segmentation enables simultaneous processing of countless samples in inexpensive microreactors, reducing both manufacturing complexity and per-sample cost through economies of scale
2Productivity
If emulsion PCR is used for clonal amplification, then sequencing throughput is improved, but phase errors occur leading to short read lengths
Solution Approach 1:
The patent performs clonal amplification via emulsion PCR before sequencing to ensure sufficient template copies are present in each droplet. This preliminary amplification step guarantees that when sequencing begins, there are enough identical template molecules to maintain signal strength and accuracy throughout the entire read length, preventing phase errors
Solution Approach 2:
The system monitors sequencing signal strength across cycles and uses this feedback to detect when template copies are being depleted. By tracking the consensus sequence across multiple template copies in each droplet, the system can identify and correct phase errors, maintaining high accuracy and extended read lengths even as amplification progresses
3Device complexity
If reusable systems are employed, then device complexity and engineering sophistication increase, but cost-effectiveness improves
Solution Approach 1:
The patent employs reusable microfluidic chips and imaging systems that can perform multiple functions: droplet generation, emulsion PCR amplification, and sequencing detection. These universal platforms can be reused across countless sequencing reactions, amortizing the high engineering and manufacturing costs over large numbers of samples, thereby improving cost-effectiveness
Solution Approach 2:
The system merges multiple functions into integrated reusable devices: the microfluidic chip combines droplet formation, amplification, and sequencing capabilities; the imaging system integrates optical detection with real-time data processing. This consolidation reduces per-reaction costs by eliminating the need for separate disposable components while maintaining high throughput through sophisticated engineering
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
These methods enable accurate and cost-effective high-throughput DNA sequencing with extended read lengths by correcting phase errors and utilizing reusable systems, enhancing the sensitivity and efficiency of genetic and biological analysis.
Implementation Method 1
sequencing a first portion of a population of target polynucleotides
Implementation Method 2
electronic detection of nucleotide incorporation
Implementation Method 3
adding one or more oligonucleotide clamps, the clamp(s) hybridizing to the target polynucleotides to halt the sequencing reaction
Data Source
AI summary
The invention relate to systems and methods for sequencing polynucleotides, as well as detecting reactions and binding events involving other biological molecules. The systems and methods may employ chamber-free devices and nanosensors to detect or characterize such reactions in high-throughput. Because the system in many embodiments is reusable, the system can be subject to more sophisticated and improved engineering, as compared to single use devices.