Capture Probes for Nucleic Acid Isolation via Hybridization
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Solution Overview
Problem
Existing methods for nucleic acid isolation are often complex, require harsh chemicals, and are time-consuming, making it difficult to efficiently separate target nucleic acids from other sample components.
Innovation Solution
A population of capture probes is used, comprising a first region with a poly(r) sequence, either randomized or non-randomized, and a second region with a specific binding partner (SBP) capable of binding to an immobilized probe, allowing for the specific isolation of target nucleic acids.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional nucleic acid isolation methods are used, then target nucleic acids can be isolated, but the procedures are complex and time-consuming
Solution Approach 1:
The patent introduces a bridge oligonucleotide as an intermediary component that mediates between the target nucleic acid and the solid support. The bridge oligonucleotide contains a first binding domain that hybridizes to the target nucleic acid and a second binding domain that binds to the solid support, thereby simplifying the isolation procedure into a single hybridization step while maintaining high efficiency
Solution Approach 2:
The bridge oligonucleotide is designed with universal binding characteristics that allow it to work with various target nucleic acids regardless of their specific sequences. The first binding domain can hybridize to different target sequences, making the method universally applicable to diverse nucleic acid isolation scenarios without requiring method redesign
2Object-affected harmful factors
If traditional nucleic acid isolation methods are used, then target nucleic acids can be isolated, but harsh chemicals are required
Solution Approach 1:
The patent replaces harsh chemical treatments with a hybridization-based mechanical binding system. Instead of using denaturing chemicals to separate nucleic acids from other components, the method uses specific hybridization between the bridge oligonucleotide and target nucleic acid, followed by solid support binding, thereby eliminating the need for harsh chemicals while maintaining isolation efficiency
Solution Approach 2:
The bridge oligonucleotide acts as a mediator that enables selective binding through hybridization without requiring harsh chemical conditions. It facilitates the separation of target nucleic acids from complex samples using mild hybridization buffers, thus reducing chemical harshness while preserving nucleic acid integrity
3Adaptability or versatility
If specific oligonucleotides are designed for each target, then specific targets can be isolated, but the design and optimization becomes complex
Solution Approach 1:
The oligonucleotide is segmented into distinct functional domains: a first binding domain for target hybridization, a second binding domain for solid support attachment, and optional linker regions. This segmentation allows independent optimization of each domain's function, simplifying the overall design process while maintaining high target specificity and binding efficiency
Solution Approach 2:
The bridge oligonucleotide design provides universality by using a standardized second binding domain that consistently binds to the solid support across different applications. This universal component reduces design complexity by eliminating the need to redesign the solid support interaction portion for each new target, allowing focus only on the target-specific first binding domain
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 enables efficient and rapid isolation of target nucleic acids from complex samples, reducing the need for harsh chemicals and complex procedures, and allowing for the capture of both known and unknown target sequences.
Implementation Method 1
a first region that is at least about 12 residues in length and comprises at least one poly(r) sequence
Implementation Method 2
a second region comprising a first specific binding partner (SBP), wherein the SBP is capable of specifically binding a second specific binding partner (SBP2)
Data Source
AI summary
Populations of target capture probes are provided that are useful for nucleic acid separation and purification. The probes of the population comprise a first region that is at least about 12 residues in length and comprises a poly(r) sequence comprising (i) a randomized sequence comprising G and A nucleotides, or (ii) a non-randomized repeating (A and G) sequence; and a second region comprising a first specific binding partner (SBP), wherein the SBP is capable of specifically binding a second specific binding partner (SBP2). Related combinations, methods, uses, kits, and reaction mixtures are also provided.