Nucleic Acid Capture Probe Hybridization Specificity
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Solution Overview
Problem
Current nucleic acid sequencing methods face inefficiencies in library construction and probe capture, particularly due to non-specific hybridization and varying adapter requirements across different sequencing platforms, which affect the proportion of effective sequencing data.
Innovation Solution
A method for capturing nucleic acid molecules with a probe that utilizes complementary strands with a single-stranded end, optimizing hybridization by controlling melting temperatures and immobilizing probes on solid bases for improved specificity and efficiency, allowing for both double-stranded and single-stranded capture and subsequent sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If probe capture method is used to capture target sequence, then specific region can be selectively isolated, but non-specific hybridization occurs reducing capture efficiency
Solution Approach 1:
The patent introduces a temperature parameter (Tm difference of 20-40°C between first and second strands) to control hybridization specificity. By maintaining the first strand in a single-stranded state through temperature control, the probe can specifically hybridize to the target sequence without non-specific binding to the second strand, thus resolving the contradiction between capture specificity and capture efficiency.
2Ease of manufacture
If different adapters are optimized for different sequencing platforms, then ligation efficiency is improved, but library construction complexity increases
Solution Approach 1:
The patent designs a universal adapter structure containing a first nucleic acid strand with a 5' phosphate group and a second nucleic acid strand, where the first strand serves multiple functions: it provides ligation capability, maintains single-stranded state for probe hybridization, and enables platform-independent library construction. This universal design eliminates the need for platform-specific adapter optimization, reducing library construction complexity while maintaining high ligation efficiency.
3Stability of the object's composition
If double-stranded nucleic acid molecules are used for sequencing, then stability is improved, but probe hybridization efficiency decreases
Solution Approach 1:
The patent utilizes temperature parameter control to maintain the first nucleic acid strand in a single-stranded state with a Tm difference of 20-40°C relative to the second strand. This allows the double-stranded molecule to remain stable overall while the first strand remains accessible for probe hybridization, thus resolving the contradiction between stability and hybridization efficiency.
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 enhances the capture efficiency of nucleic acid libraries, reducing non-specific hybridization and increasing the proportion of effective sequencing data, with improved hybridization and sequencing outcomes.
Implementation Method 1
the probe and the target sequence, and the target sequence captured is often a single-stranded sequence
Data Source
Figure 1
AI summary
A method for capturing a nucleic acid molecule, and a use therefor. Disclosed in the present application is a method for capturing a nucleic acid molecule, the nucleic acid molecule consisting of a first nucleic acid strand and a second nucleic acid chain. The first nucleic acid chain and the second nucleic acid strand are partially matched to form a double-stranded region, and at least one end of the nucleic acid molecule is a single-stranded region. The method comprises make contact between a probe with and nucleic acid molecule, causing the probe to bind with the single-stranded region of the nucleic acid molecule, and forming a hybrid complex. A preparation method for a nucleic acid library is also disclosed.