Microstructured Solid Phase for Spatially Resolved DNA Amplification
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Solution Overview
Problem
Current nucleic acid amplification and sequencing technologies face challenges such as complex processes, high costs, and inefficiencies in spatially separating and immobilizing sample fragments, leading to contamination, sample loss, and limited analysis capabilities, especially for low-redundancy samples and long DNA fragments.
Innovation Solution
A microstructured fixed phase with catcher molecules immobilized on its surface is used to amplify nucleic acid fragments independently in separate compartments, allowing for spatial separation and immobilization during the amplification process, reducing contamination and sample loss, and enabling efficient parallel analysis of multiple samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If oil-in-water emulsion microcompartments are used for amplification, then spatial separation of sample fragments is achieved, but the process becomes complex and requires separate immobilization steps
Solution Approach 1:
The patent combines the amplification reaction and immobilization steps into a single integrated process. The solid phase support structure allows DNA fragments to be amplified and simultaneously immobilized on the same solid phase, eliminating the need for separate emulsion formation and subsequent bead handling steps required in traditional emPCR methods.
Solution Approach 2:
The patent extracts the aqueous amplification environment from the oil emulsion context and performs PCR directly on a solid phase. This removes the need for oil phase components and emulsion formation while maintaining spatial separation through the solid phase structure itself.
2Reliability
If separate immobilization steps are used after amplification, then amplicons can be fixed on solid phase, but sample loss and contamination increase
Solution Approach 1:
The patent performs immobilization concurrently with the amplification reaction rather than as a subsequent step. The solid phase structure is already in place during amplification, so amplicons are immobilized as they are generated, preventing sample loss that would occur during transfer and handling in multi-step processes.
3Reliability
If microspheres are used for amplification, then spatial arrangement is achieved, but costs increase and handling becomes complex
Solution Approach 1:
The patent uses a disposable solid phase support structure (such as a microarray slide or chip) that can be manufactured at low cost using standard semiconductor or microfabrication techniques. This replaces expensive, specialized microspheres that require complex handling equipment, while achieving the same spatial arrangement function through fixed positioning on the solid phase.
4Productivity
If traditional emPCR is used, then amplification of DNA fragments is achieved, but analysis of long DNA fragments and low-redundancy samples is limited
Solution Approach 1:
The patent creates locally optimized conditions on the solid phase surface that favor the amplification and retention of long DNA fragments. The solid phase geometry and surface chemistry can be tailored to accommodate larger molecular sizes, and the direct immobilization prevents the mechanical stress and dilution effects that limit traditional emPCR for long fragments and low-abundance samples.
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 simplifies the amplification and immobilization process, reduces costs, and allows for longer DNA fragments to be amplified, providing faster and more efficient analysis with higher accuracy and longer DNA sequencing capabilities compared to existing methods.
Implementation Method 1
compartmentalization of aqueous reaction phases on a solid phase
Implementation Method 2
capture molecules, to which an amplicon is bound
Data Source
Figure 1
Figure 2A~2D
Figure 3H~3I
AI summary
The invention relates to a method for performing a biochemical or chemical reaction for an isolated, spatially separated amplification of sample fragments during a simultaneous immobilization and spatial arrangement of the sample fragments and reaction products, the amplification products, on one or more suitable solid phases for subsequent derivatizations.