Flow Cell Surface Segmentation for Sequencing Signal Resolution
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Solution Overview
Problem
Simultaneous paired-end sequencing technologies face challenges in reducing the padlock-like conformation of primer sets on flow cell surfaces, which leads to signal interference and decreased resolution in nucleic acid sequencing.
Innovation Solution
The use of polymeric hydrogels to attach different primer sets to specific regions of a flow cell surface, ensuring orthogonal cleaving chemistry and spatial separation of forward and reverse strands to minimize padlock-like configurations, thereby improving signal resolution.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If primer sets are attached to different regions within each depression on the flow cell surface, then simultaneous paired-end sequencing can be performed, but padlock-like conformations form causing signal interference and decreased resolution
Solution Approach 1:
The flow cell surface is divided into multiple distinct regions within each depression, with each region containing a specific primer set (e.g., P1-R1, P2-R2). This segmentation prevents padlock-like conformations by ensuring that forward and reverse primers are spatially separated into different regions, thereby eliminating signal interference while enabling simultaneous paired-end sequencing
Solution Approach 2:
Different regions within each depression are assigned different functional properties by attaching specific primer sets to each region. The first region contains forward primers (P1, P2) while the second region contains reverse primers (R1, R2), creating localized functional zones that prevent unwanted primer interactions and maintain signal resolution
2Adaptability or versatility
If different primer sets are attached to the flow cell surface, then paired-end sequencing is enabled, but signal contamination occurs between forward and reverse reads
Solution Approach 1:
The flow cell surface is segmented into distinct regions, each containing specific primer sets. This spatial segmentation ensures that forward and reverse primers are physically separated, preventing padlock-like conformations and the resulting signal contamination between reads while maintaining full paired-end sequencing capability
Solution Approach 2:
The flow cell surface acts as an intermediary structure that mediates the spatial organization of primer sets. By providing distinct attachment regions on the flow cell surface, the system prevents direct unwanted interactions between forward and reverse primers, thereby eliminating signal contamination
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 enhances signal resolution by reducing or eliminating padlock-like conformations, allowing for simultaneous base calling of both reads without signal contamination, thus improving the accuracy of nucleic acid sequencing.
Implementation Method 1
different primer sets are attached to different regions within each depression and/or on each protrusion of a flow cell surface through polymeric hydrogel(s)
Data Source
AI summary
A metal film is formed over a resin layer including a plurality of multi-depth depressions (MDP) separated by interstitial regions, each MDP including a deep portion and an adjacent shallow portion. A sacrificial layer is formed over the metal film. The sacrificial layer and metal film are sequentially dry etched to expose a resin layer surface at the shallow portion and interstitial regions. Resin layer portions are removed i) at the shallow portion to form a depression region having a surface directly adjacent to a surface at the deep portion and ii) at the interstitial regions to form new interstitial regions surrounding the deep portion and the depression region. First functionalized layer is deposited over the metal film, depression region, and new interstitial regions. The metal film is removed from the deep portion. Second functionalized layer is deposited over the surface at the deep portion. New interstitial regions are polished.