Azido Organosilane Surface Functionalization Without Hydrogel Lift-Off
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Solution Overview
Problem
Existing methods for surface functionalization in DNA sequencing, such as using hydrogels, are cumbersome and prone to incomplete lift-off, leading to instability and inefficiencies in DNA clustering and sequencing-by-synthesis chemistry.
Innovation Solution
A substrate with a surface-bound organosilane layer containing azido groups attached through a linker moiety, free from hydrogels or hydrophilic polymers, is used for immobilizing oligonucleotides, allowing direct covalent attachment without the need for hydrogel coatings.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If hydrogel coating is used for surface functionalization, then DNA clustering and sequencing chemistry can be enabled, but the process becomes cumbersome and incomplete lift-off occurs
Solution Approach 1:
The patent removes the hydrogel coating layer from the surface functionalization process, extracting the problematic intermediate layer that caused incomplete lift-off and process complexity. The invention directly functionalizes the solid support surface with silane-based chemistry, eliminating the need for hydrogel as a intermediary coating layer.
Solution Approach 2:
The patent introduces a silane-based intermediary layer that directly bonds to the solid support surface and provides the necessary functional groups for DNA clustering. This silane layer serves as the mediator between the solid support and the biological molecules, replacing the hydrogel intermediary that caused problems.
2Ease of manufacture
If hydrogel coating is applied to solid support, then primer immobilization is enabled, but multiple fabrication steps are required
Solution Approach 1:
The patent extracts and removes the hydrogel coating step from the fabrication process, eliminating multiple sequential steps for hydrogel deposition, pattern transfer, and lift-off. The invention implements a direct silane-based functionalization approach that reduces the process to fewer critical steps.
Solution Approach 2:
The patent performs preliminary surface treatment and silane coupling directly on the solid support before primer immobilization. By preparing the surface with the appropriate silane functional groups in advance, the subsequent primer attachment step becomes simpler and faster, eliminating the need for hydrogel intermediate steps.
3Manufacturing precision
If hydrophobic polymer coating is used to retain gel material, then differential hydrophobic/hydrophilic characteristics are exploited, but unintended consequences and challenges arise
Solution Approach 1:
The patent removes the hydrophobic polymer coating layer that was used to retain gel material through differential hydrophobicity. Instead, the invention uses directly patterned silane functionalization that provides precise gel material placement without relying on hydrophobic/hydrophilic contrast mechanisms that caused unintended consequences.
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 substrate fabrication process, enhances stability, and enables efficient DNA clustering and sequencing-by-synthesis chemistry by eliminating the challenges associated with hydrogel coatings.
Implementation Method 1
depositing an organosilane to the surface of the substrate to form a surface-bound organosilane layer
Implementation Method 2
reacting the plurality of the oligonucleotides with the azido groups of the organosilane to covalently attach the oligonucleotides to the substrate
Data Source
AI summary
Embodiments of the present application relate to substrate comprising a surface-bound azido functionalized organosilane wherein the substrate is free or substantially free of a hydrogel or a hydrophilic polymer. Methods of preparing such substrate surface for sequencing applications are also disclosed.