Capture Oligomer Design for Controlled Nucleic Acid Isolation
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Solution Overview
Problem
Existing methods for nucleic acid capture are inefficient, often requiring time-consuming quantification and concentration steps, leading to issues like saturation of solid supports and complex addition of adaptors, and fail to provide a controlled amount of nucleic acid for sequencing, resulting in poor library quality and wasted bandwidth.
Innovation Solution
The use of capture oligomers with target-dependent capture mechanisms and secondary capture reagents, along with streamlined addition of adaptors, to control the amount of nucleic acid capture and improve sequencing efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing nucleic acid capture methods are used, then nucleic acid can be captured from samples, but the process requires time-consuming quantification and concentration steps, and may result in saturation of solid supports
Solution Approach 1:
The capture oligomers are pre-designed with built-in capture sequences and target-specific sequences that enable direct capture without preliminary quantification. The oligomers are prepared in advance with controlled amounts to match expected target concentrations, eliminating the need for time-consuming quantification and concentration adjustment steps before capture.
Solution Approach 2:
The capture oligomers automatically adjust their binding capacity based on target availability. When target polynucleotides are present, the capture oligomers bind specifically without requiring external control of capture oligomer concentration. The system self-regulates to prevent solid support saturation while maintaining efficient capture.
2Productivity
If excess capture oligomer is used, then capture efficiency may increase, but saturation of solid supports occurs
Solution Approach 1:
The capture oligomers incorporate variable parameters including different capture sequence affinities, lengths, and concentrations that can be optimized for specific applications. The oligomer design allows tuning of binding characteristics to match target abundance, enabling efficient capture without excess oligomer that would cause solid support saturation.
Solution Approach 2:
Instead of using excess capture oligomer to ensure complete target capture, the invention uses precisely controlled amounts of capture oligomer that are sufficient for complete target binding. The oligomer quantity is calculated based on expected target concentration and capture sequence affinity, providing optimal capture efficiency without overwhelming the solid support capacity.
3Manufacturing precision
If a defined amount of nucleic acid is required for sequencing, then library quality improves, but existing methods require additional concentration or dilution steps that are slow
Solution Approach 1:
The capture oligomers are pre-prepared in defined amounts that correspond to optimal sequencing library requirements. The capture process directly produces nucleic acid at the desired concentration and quantity, eliminating post-capture concentration or dilution steps. This preliminary preparation of capture oligomers in precise amounts ensures both library quality and workflow speed.
Solution Approach 2:
The invention merges the capture function with the quantification and concentration control functions into a single step. The capture oligomers simultaneously perform target binding and provide the nucleic acid in the precise amount needed for sequencing, combining multiple previously separate operations into one efficient process that maintains library quality while accelerating workflow.
4Ease of operation
If capture oligomers are used without target-dependent mechanisms, then capture is simpler, but control over captured amount is poor
Solution Approach 1:
The capture oligomers are designed with dual functionality: a capture sequence for binding to solid supports and target-specific sequences for specific target polynucleotide binding. This multi-functional design allows the same oligomer to perform both capture and quantification control functions, maintaining simplicity while achieving precise control over captured amount through the target-specific recognition.
Solution Approach 2:
The capture oligomers incorporate target-dependent capture mechanisms where the presence and amount of target polynucleotide directly influence the capture efficiency. The target-specific sequences ensure that capture oligomers bind only when complementary targets are present, providing automatic feedback control that prevents capture of excess nucleic acid and ensures accurate quantification without complex procedures.
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 enables rapid and accurate capture of nucleic acids in a controlled manner, ensuring optimal sequencing results by avoiding polyclonal populations and reducing dimer formation, thus enhancing data output and library quality.
Implementation Method 1
a capture oligomer, in which a defined amount of a capture oligomer or another limiting reagent (e.g., a secondary capture reagent) or a combination thereof can control the output of a capture procedure and the capture oligomer becomes captureable in a target-dependent manner
Implementation Method 2
combinations of capture oligomers and other oligomers, and related compositions, kits, and methods are provided herein for capturing and/or controlling the amount of a nucleic acid
Data Source
Figure 1A~1B
Figure 1C
Figure 2A
AI summary
Provided herein are oligomers, compositions, kits, and methods for capturing target polynucleotides, e.g., for downstream applications such as amplification, library preparation, or sequencing. In some embodiments, a capture oligomer is provided or used that comprises a capture sequence that is annealed to a complement that prevents capture until the complement is displaced in a target-polynucleotide dependent manner. In some embodiments, an amount of target polynucleotide is captured that is less than or equal to a predetermined amount.