Flowcell Microretainers for Controlled DNA Template Spacing
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Solution Overview
Problem
Current DNA sequencing instruments face challenges in controlling the spacing of DNA template colonies within flowcells, leading to inefficient data acquisition and amplification processes due to random bead placement and inefficient bead capture properties.
Innovation Solution
A flowcell design featuring a capture substrate with microretainers configured to hold microspots, providing controlled spacing and primer functionalization, along with a microfluidic particle separator using micropillars to manage microspots and enhance reagent access and DNA template amplification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If DNA template colonies are secured to individual beads in a random pattern, then the flowcell can hold the DNA template colonies, but the spacing of the beads cannot be controlled, making data acquisition more difficult
Solution Approach 1:
The flowcell substrate is divided into an array of discrete microwells, each capable of holding a single bead or DNA template colony. This segmentation allows precise control over the spacing and positioning of individual templates, transforming the random placement problem into a controlled array structure that facilitates systematic data acquisition.
Solution Approach 2:
Each microwell in the array provides a localized environment with specific spacing characteristics. The microwells are designed with uniform dimensions and spacing, creating consistent local conditions throughout the flowcell that enable controlled and reproducible data acquisition across all positions.
2Productivity
If gel is removed from interstitial space between wells, then DNA template colonies can be amplified in situ, but gel removal costs increase and accidental removal decreases primer density
Solution Approach 1:
The gel is extracted or removed from the interstitial spaces between the microwells, leaving only the functionalized gel within the individual microwells where it is needed for primer binding and DNA template amplification. This extraction eliminates the harmful presence of gel in non-well regions while preserving its beneficial function within wells.
Solution Approach 2:
The potential harm of gel remaining in interstitial spaces (causing unwanted amplification or blocking) is converted into a benefit by selectively removing gel from those regions. The gel that remains in microwells continues to provide primer binding functionality, while its removal from interstitial areas prevents unwanted side effects.
3Quantity of substance
If microretainers are spaced close together, then more microspots can be held per unit area, but the interstitial gap distance decreases, potentially allowing microspots to migrate
Solution Approach 1:
The microretainers are designed with three-dimensional structures (such as wells or pillars) that extend vertically from the substrate surface. This vertical dimension provides retention capability without requiring large horizontal spacing, allowing high microspot density while maintaining reliable retention through the depth of the microretainer structures.
Data Source
AI summary
A flowcell for a sequencing instrument. The flowcell includes a fluid inlet, a fluid outlet, a flow channel formed between an at least partially transparent cover and a base and fluidly connecting the fluid inlet to the fluid outlet, and a capture substrate provided in the flow channel. The capture substrate includes microretainers configured to each receive a single microspot having a microspot diameter, and microretainer is separated from adjacent microretainers by an interstitial gap distance that is equal to or greater than the microspot diameter. A particle separator may be fluidly connected to the flowcell. The particle separator may include a microfluidic channel having an array of micropillars to transfer a plurality of the microspots to a loading buffer that may be delivered to the flowcell.