Multivalent Oligonucleotide Assemblies for Efficient Target Hybridization
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Solution Overview
Problem
Existing targeted sequencing techniques face challenges with low manufacturing efficiency and high cost of longer oligonucleotide probes due to secondary structures and poor synthesis yields, leading to inefficient capture of target nucleic acids.
Innovation Solution
The use of multivalent assemblies comprising multiple shorter oligonucleotide probes that target different regions of a nucleic acid, enhancing hybridization avidity and avoiding secondary structures, which are immobilized on a surface such as a bead or a bead surface, to achieve efficient target enrichment.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If longer oligonucleotide probes are used to improve target capture specificity, then hybridization specificity is improved, but manufacturing efficiency deteriorates due to secondary structures and poor synthesis yields
Solution Approach 1:
The patent divides a single long probe into multiple shorter probes (e.g., three probes of 15-30 nucleotides each) that target different regions of the same target sequence. This segmentation maintains hybridization specificity through multiple binding sites while improving manufacturing efficiency by reducing secondary structure formation and increasing synthesis yields of individual shorter probes.
2Measurement precision
If longer oligonucleotide probes are used to improve target capture specificity, then hybridization specificity is improved, but cost increases due to poor synthesis yields
Solution Approach 1:
The patent segments the probe into multiple shorter oligonucleotides, each with improved synthesis yields and lower costs. The cumulative effect of multiple shorter probes achieves the same specificity as a single long probe while reducing material losses and synthesis costs.
Solution Approach 2:
The patent changes the length parameter of the probes from long (resulting in poor synthesis) to short (resulting in good synthesis). By optimizing the length of individual probes to 15-30 nucleotides, the synthesis yield improves while maintaining adequate hybridization specificity through multiple probes.
3Ease of manufacture
If multiple shorter oligonucleotide probes are used to improve synthesis yields, then manufacturing efficiency is improved, but hybridization avidity must be maintained through multivalent assembly
Solution Approach 1:
The patent merges multiple shorter probes into a single multivalent assembly (e.g., on a bead or nanoparticle). This combination provides multiple hybridization sites that collectively bind the target sequence, maintaining high avidity equivalent to or exceeding that of a single long probe while benefiting from the improved synthesis yields of shorter individual probes.
Solution Approach 2:
The patent creates a composite structure combining multiple oligonucleotide probes with a solid support (bead, nanoparticle, or other carrier). This composite multivalent assembly provides both the manufacturing advantages of shorter probes and the binding avidity of multiple simultaneous hybridization events.
4Productivity
If multivalent assemblies with multiple probes are used to enhance hybridization avidity, then target capture efficiency is improved, but device complexity increases
Solution Approach 1:
The patent combines multiple probes onto a single multivalent platform (bead or nanoparticle), which simplifies the overall system architecture compared to using separate probes or arrays. The multivalent assembly integrates multiple functions into a single reagent unit, improving target capture efficiency while managing complexity through consolidation.
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 improves synthesis yields and reduces probe requirements while maintaining high binding affinity, allowing for faster hybridization kinetics and more uniform hybridization strength, thereby enhancing target capture efficiency.
Implementation Method 1
a first single-stranded oligonucleotide probe complementary to a first region of a target nucleic acid, a second single-stranded oligonucleotide probe complementary to a second region of the target nucleic acid, and a third single-stranded oligonucleotide probe complementary to a third region of the target nucleic acid
Data Source
AI summary
Multivalent assemblies for target hybridization are described. The multivalent assemblies include oligonucleotide sets that hybridize to a target nucleic acid to permit capture of the target nucleic acid. In an embodiment, the multivalent assemblies are heteromultivalent such that the oligonucleotide sets include different oligonucleotides that bind to different regions of the target nucleic acid.