Multi-depth Nanowell Patterning via Resin Photomasks
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Solution Overview
Problem
Current nanopatterning processes for DNA sequencing are complex and costly, particularly in preparing substrates for simultaneous paired-end reading methods, which require multiple layers and etch steps to achieve spatial separation of DNA strands.
Innovation Solution
A patterned substrate with multiple resin layers, where a first resin layer allows light passage, a second resin layer acts as a photomask to block light, and a third resin layer allows light passage, enabling the creation of multi-level depressions with deep and shallow wells. This configuration allows for the selective curing and removal of photoresist within these depressions, simplifying the patterning process and eliminating the need for temporary sacrificial masks.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If multiple etch steps and temporary sacrificial masks are used to achieve spatial separation of DNA strands, then sequencing precision is improved, but device complexity and manufacturing cost increase
Solution Approach 1:
The substrate is segmented into multiple resin layers (first resin layer, second resin layer, third resin layer) with different optical properties. The first and third resin layers allow light passage while the second resin layer blocks light, creating spatially separated deep wells and shallow wells that can simultaneously accommodate forward and reverse DNA strands without requiring complex temporary masks or multiple etch steps.
Solution Approach 2:
The patent transitions from a two-dimensional patterning approach to a three-dimensional multi-level structure. By creating deep wells and shallow wells at different depths within the substrate, the patent achieves spatial separation of DNA strands in the vertical dimension, eliminating the need for complex lateral separation methods involving multiple etch steps and sacrificial masks.
2Measurement precision
If multiple nanopatterning steps involving several layers of materials are used, then spatial separation of DNA strands is achieved, but manufacturing time and cost increase
Solution Approach 1:
The multi-layer resin structure is pre-configured with alternating light-permeable and light-blocking layers before the actual sequencing process. This preliminary structuring creates the deep well and shallow well configurations in advance, eliminating the need for time-consuming temporary mask applications and multiple etch steps during sequencing preparation.
Solution Approach 2:
The patent extracts and eliminates the need for temporary sacrificial masks from the patterning process. By using the multi-layer resin structure itself to define the deep and shallow wells, the patent removes the additional steps of applying, positioning, and removing temporary masks, thereby reducing manufacturing time and complexity.
3Ease of manufacture
If a simple single-layer resin structure is used, then manufacturing simplicity is improved, but spatial separation capability for simultaneous paired-end reading is lost
Solution Approach 1:
Each resin layer serves multiple functions: the first resin layer provides structural support and light transmission, the second resin layer provides light blocking and structural definition, and the third resin layer provides additional light transmission and structural completion. This multi-functionality allows the multi-layer structure to achieve spatial separation capability while maintaining manufacturing simplicity through a systematic, repeatable fabrication process.
Solution Approach 2:
The patent uses composite resin materials with different optical properties (light-permeable vs. light-blocking) arranged in alternating layers. This composite structure enables spatial separation of DNA strands by creating regions of different light transmission characteristics, while the systematic layering maintains ease of manufacture through a unified fabrication approach.
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 solution simplifies the substrate patterning process, reduces costs, and enhances the efficiency of DNA sequencing by allowing for the simultaneous sequencing of forward and reverse DNA strands without the complexity of multiple etch steps, thereby reducing sequencing time.
Implementation Method 1
a first resin layer positioned over the base support, the first resin layer configured to allow passage of light
Implementation Method 2
a second resin layer positioned over the first resin layer, the second resin layer configured as a photomask for blocking passage of light
Implementation Method 3
exposing the substrate to light from a backside of the base support opposite to the imprint layer such that only the photoresist residing within the deep wells of the multi-level depressions are cured
Data Source
AI summary
Embodiments of the present disclosure relate to patterned substrates with functionalized surface such as flow cells, as well as methods of fabricating the patterned substrate. In particular, patterned substrates of the present disclosure may be prepared using two or more imprint resin layers, one of which acts as a photomask for the photoresist during substrate patterning, without the need of any metallic photomask. Embodiments of the patterned substrate may be used for simultaneous paired-end sequencing methods.