Sequencing Chip Surface Treatment to Reduce Random Nucleotide Adsorption
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Solution Overview
Problem
The high signal-to-noise ratio on sequencing surfaces leads to random adsorption of nucleotides, causing sequencing errors and reduced accuracy, particularly affecting sites with fewer nucleic acid templates.
Innovation Solution
Using phosphoric acid compounds with specific structures to treat the sequencing chip surface, forming stable complexes with oligonucleotides to reduce non-specific adsorption and compete with nucleotides for binding sites.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If the sequencing surface is used to detect fluorescence signals, then the sequencing reaction can be performed, but the random adsorption of nucleotides on the surface increases the signal-to-noise ratio and causes sequencing errors
Solution Approach 1:
The patent introduces a blocking agent as an intermediary substance that selectively binds to the solid carrier surface to prevent nucleotide adsorption. The blocking agent acts as a mediator between the nucleotides and the surface, occupying binding sites without interfering with the sequencing reaction, thereby reducing random adsorption and improving sequencing accuracy
Solution Approach 2:
The patent modifies the surface properties of the solid carrier by changing the chemical or physical parameters of the surface through treatment with blocking agents. This alters the surface chemistry to reduce non-specific binding of nucleotides while maintaining the ability to support the sequencing reaction, effectively lowering the signal-to-noise ratio
2Manufacturing precision
If the surface has linker sequences randomly immobilized, then the oligonucleotide can be bound to the surface, but free nucleotides are easily randomly adsorbed increasing the error rate
Solution Approach 1:
The blocking agent serves as an intermediary that selectively interacts with the solid carrier surface rather than with the oligonucleotide or nucleotides during the sequencing reaction. This intermediary approach allows the oligonucleotide to remain properly immobilized while preventing free nucleotides from randomly adsorbing to the surface, thus maintaining manufacturing precision while reducing sequencing errors
Solution Approach 2:
The patent applies blocking agents in advance to the solid carrier surface to preemptively occupy binding sites that would otherwise be available for random nucleotide adsorption. This preliminary anti-action prevents the harmful adsorption before it can occur during the sequencing reaction, reducing the error rate while preserving the intended oligonucleotide binding
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
Reduces sequencing errors by minimizing non-specific adsorption, improving sequencing accuracy and throughput, especially for low-template sites.
Implementation Method 1
the phosphoric acid compound binds to the oligonucleotide to form a stable complex to enclose the reactivity of the oligonucleotide... the random adsorption of a nucleotide substrate on the surface of a sequencing chip
Data Source
AI summary
Provided are a surface treatment method, a sequencing method, and a kit for nucleic acid molecule extension. The surface treatment method comprises: contacting a phosphate compound with a surface bound with an oligonucleotide, wherein the phosphate compound comprises a compound having a structural formula represented by formula (1) and/or formula (2). With regard to the problem that bases are prone to random adsorption on the surface of the sequencing chip in the sequencing process, it has been unexpectedly discovered that compounds with a specific structure can compete with virtual terminator bases in the sequencing process for adsorption on the surface of the sequencing chip, thus reducing the random adsorption of bases on the surface of the sequencing chip, reducing the resultant sequencing error rate, and improving the sequencing throughput.