Paired-End Sequencing via Solid Support Anchoring
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Solution Overview
Problem
Current paired-end sequencing methods are costly, time-consuming, and complex, limiting their efficiency and throughput in generating high-quality genomic data.
Innovation Solution
A method involving immobilizing target nucleic acid on a solid support, generating a complementary strand with a linkable moiety, and comparing sequences to obtain paired-end sequencing information, which simplifies the process by minimizing undesirable hybridization and anchoring the complementary strand to the support, allowing for efficient sequencing reads.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional paired-end sequencing methods are used, then sequencing accuracy is improved, but cost increases and throughput decreases
Solution Approach 1:
The method segments the paired-end sequencing process into distinct phases: first sequencing one end of the fragment while it's attached to the solid support, then releasing and re-attaching the fragment to sequence the other end. This segmentation allows independent optimization of each sequencing reaction and improves overall throughput while maintaining accuracy.
Solution Approach 2:
The fragment is pre-attached to the solid support before sequencing begins, and the first end is sequenced while in this fixed position. This preliminary positioning enables efficient library preparation and allows the fragment to be released and re-attached for the second sequencing reaction without requiring complex real-time manipulation during sequencing.
2Measurement precision
If traditional paired-end sequencing methods are used, then sequencing accuracy is improved, but time consumption increases
Solution Approach 1:
The method maintains continuous useful action by keeping fragments attached to the solid support throughout the process. The first sequencing reaction proceeds while fragments are anchored, then fragments are released and immediately re-attached for the second reaction, eliminating idle time and ensuring the sequencing instrument operates continuously without interruption.
Solution Approach 2:
Library preparation and fragment attachment are performed in advance before sequencing begins. This preliminary action allows the sequencing instrument to start immediately with the actual sequencing reactions, reducing overall time consumption while maintaining the accuracy benefits of paired-end sequencing.
3Reliability
If traditional paired-end sequencing methods are used, then data quality is improved, but process complexity increases
Solution Approach 1:
The solid support serves multiple functions: it anchors fragments during library preparation, holds fragments during the first sequencing reaction, and provides a platform for re-attachment after release. This multi-functionality simplifies the overall process by eliminating the need for separate devices or complex manipulation steps, reducing process complexity while maintaining data quality.
Solution Approach 2:
The method extracts and separates the two sequencing reactions into distinct, independent steps. The fragment is sequenced at one end while attached, then released and re-attached for sequencing at the other end. This extraction simplifies the process by allowing each sequencing reaction to be optimized independently and performed under standard conditions, reducing overall process complexity.
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 method reduces the complexity and time required for paired-end sequencing, improving data quality and throughput while minimizing costs by using a simpler protocol that anchors the complementary strand to the solid support, enabling more accurate read alignment and detection of genomic rearrangements.
Implementation Method 1
The target nucleic acid is hybridized to a surface oligonucleotide on the solid support
Implementation Method 2
the solid support comprises at least one corresponding linkable moiety for selectively covalently or non-covalently binding the at least one linkable moiety on the complementary nucleic acid strand
Implementation Method 3
the at least one linkable moiety comprises a nucleic acid sequence substantially complementary to the surface oligonucleotide
Implementation Method 4
determining the sequence of the target nucleic acid by generating a complementary nucleic acid strand
Data Source
Figure 1A~1B
Figure 2A~2C
Figure 2D~2E
AI summary
A method of obtaining paired-end sequencing information in a sequencing reaction in which a single stranded target nucleic acid is immobilized on a solid support and the sequence of the single stranded target nucleic acid is determined by generating a complementary nucleic acid strand comprising at least one linkable moiety for linking the complementary strand to the solid support.