Cluster Array Micropore Device for Automated Gene Synthesis
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Solution Overview
Problem
Current gene synthesis methods face challenges such as high reagent consumption, complex mixing operations, low yield, and high costs, which hinder efficient and automated high-throughput gene assembly.
Innovation Solution
A high-throughput gene synthesis device utilizing cluster arrays with funnel-shaped or cylindrical micropores on a substrate, where each cluster of micropores corresponds to a well on a microwell plate, using solid phase carriers for oligonucleotide synthesis and a micro-nano liquid dispenser for precise chemical distribution, enabling automated synthesis and assembly of oligonucleotides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If traditional solid-phase oligonucleotide synthesis method is used, then yield is high (nanomole level), but reagent consumption is large and cost is high
Solution Approach 1:
The substrate is divided into multiple micropores arranged in clusters, with each micropore containing solid phase carriers for independent oligonucleotide synthesis. This segmentation allows parallel synthesis of multiple oligonucleotides in a single reaction system, reducing total reagent consumption while maintaining high yield through efficient space utilization.
Solution Approach 2:
The invention changes the physical state and arrangement parameters of solid phase carriers from traditional separate tubes to clustered micropores on a substrate. This parameter change enables high-throughput parallel synthesis, improving productivity while reducing reagent consumption through optimized reaction conditions in confined micropore spaces.
2Productivity
If microarray-based high-throughput synthesis method is used, then throughput is high (millions of oligonucleotide sequences), but yield is low (femtomole level) requiring PCR amplification
Solution Approach 1:
The substrate is segmented into multiple micropores arranged in clusters, with each micropore containing solid phase carriers for independent oligonucleotide synthesis. This segmentation allows parallel synthesis of multiple oligonucleotides in a single reaction system, reducing total reagent consumption while maintaining high yield through efficient space utilization.
Solution Approach 2:
The invention uses multiple solid phase carriers within each micropore as templates to synthesize identical oligonucleotide sequences simultaneously. This copying approach amplifies the yield at the source, producing sufficient quantities (picomole level) to eliminate the need for subsequent PCR amplification while maintaining high throughput.
3Quantity of substance
If microfluidic device-based synthesis is used, then synthesis yield is high (100 pmol level), but device structure is complex requiring micropump and microvalve
Solution Approach 1:
The invention extracts and eliminates the complex micropump and microvalve components from the microfluidic device, achieving high synthesis yield (100 pmol level) through a simplified structure that uses only passive fluid delivery and standard laboratory equipment, thus reducing device complexity while maintaining high productivity.
Solution Approach 2:
The micropores are designed with self-contained solid phase carriers that perform synthesis autonomously without requiring external micropumps or microvalves. The system uses gravity-driven fluid delivery and standard laboratory equipment, making the device self-sufficient and simplifying the overall structure while maintaining high synthesis yield.
4Extent of automation
If semiconductor silicon chip-based synthesis is used, then no manual mixing is required, but cost is high due to complex substrate processing technology
Solution Approach 1:
The invention uses disposable micropore structures with embedded solid phase carriers that can be easily manufactured using standard laboratory techniques rather than complex semiconductor processing. This approach maintains automation through the cluster array design while significantly reducing manufacturing cost by avoiding expensive substrate processing technology and specialized equipment.
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
The device achieves high-yield oligonucleotide synthesis at the picomole level, facilitating automated gene assembly without amplification, reducing errors, and simplifying operations, thereby addressing the limitations of existing methods.
Implementation Method 1
The inner wall surface of the micropore is chemically modified as a solid phase carrier for nucleic acid synthesis, or the micropore is filled with solid phase carriers
Data Source
AI summary
A high-throughput automated gene synthesis device based on a cluster array includes a substrate and a microwell plate; the substrate is provided with a plurality of clusters of micropores; the inner wall surface of the micropores is chemically modified as a solid phase carrier for nucleic acid synthesis, or the micropore is filled with solid phase carriers; the clusters of micropores are arranged in a cluster array and each cluster of micropores has the same size and corresponding position as each well on the microwell plate. When using the device to synthesize oligonucleotides, by automatically recovering the synthesized oligonucleotides into a standard SBS plate of the corresponding size under the device, the oligonucleotide pool for each gene is formed. The yield of oligonucleotides is in picomole level, which is used for subsequent polymerase-mediated gene assembly (PCA) or ligase-mediated gene assembly (LCR) without amplification.