Dual-Strand RNA Probe Capture for Nucleic Acid Enrichment
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Solution Overview
Problem
Existing nucleic acid sequencing technologies struggle to efficiently enrich specific target nucleic acid sequences, particularly in complex biological samples, limiting the accuracy and efficiency of genetic and genomic analysis.
Innovation Solution
A method involving RNA probe sets that target antiparallel strands of a duplex segment in nucleic acid sequences, immobilized on a solid support, allowing concurrent or sequential hybridization and capture of both strands, enhancing the enrichment process.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional nucleic acid enrichment methods are used, then the process is simpler, but the enrichment efficiency and accuracy are insufficient
Solution Approach 1:
The enrichment method is divided into two distinct steps: (1) hybridization of RNA probe sets with target nucleic acid sequences, and (2) immobilization onto solid support. This segmentation allows each step to be optimized independently, improving overall enrichment efficiency while maintaining procedural clarity
Solution Approach 2:
RNA probe sets serve as intermediaries that specifically bind to target nucleic acid sequences through hybridization. These probes act as mediators between the complex biological sample and the solid support, enabling selective capture of target sequences while simplifying the overall enrichment process
2Manufacturing precision
If only single-strand targeting is used, then the probe design is simpler, but the capture completeness is insufficient
Solution Approach 1:
Each RNA probe set is divided into two separate probes: one targeting the forward strand and another targeting the reverse strand of the target nucleic acid sequence. This segmentation ensures that both strands are captured independently, achieving complete capture while keeping each individual probe design relatively simple
Solution Approach 2:
The dual-strand RNA probe set design provides universal coverage for both forward and reverse strands of target sequences. This multi-functional approach ensures that regardless of which strand is present in the sample, the enrichment method will capture it, improving capture completeness without significantly increasing 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
The method effectively captures and enriches target nucleic acid sequences, improving the accuracy and efficiency of genetic analysis by ensuring both strands of the duplex segment are captured, thereby facilitating more precise genetic and genomic analysis.
Implementation Method 1
capturing each strand of the at least one target nucleic acid sequence from the biological sample through concurrent hybridization of the two antiparallel strands of the duplex segment in the each of the at least one target nucleic acid sequence with both the first RNA probe set and the second RNA probe set
Implementation Method 2
each RNA probe in any of the first RNA probe set and the second RNA probe set is labelled with an immobilization portion configured to allow immobilization onto the solid support. The solid support is labelled with at least one coupling partner, each capable of forming a secure coupling to the immobilization portion
Data Source
AI summary
A method and a kit for enriching target nucleic acid sequences from a biological sample are disclosed. The method includes preparing, and contacting with the biological sample, a first RNA probe set and a second RNA probe set respectively and concurrently targeting both of the two antiparallel strands of a duplex segment in each target nucleic acid sequence. Each RNA probe in the first and second RNA probe set can be generated by chemical synthesis or by in vitro or in vivo transcription, and can be biotin-labelled to thereby allow capturing of the target nucleic acid sequences by magnetic beads labelled with streptavidin, or can be engineered to a microfluidic channel to facilitate the capturing. The method can be applied to capture double-stranded nucleic acid sequences or single-stranded nucleic acid sequences having duplex segments, and the nucleic acid sequences can include DNAs, RNAs, or DNA-RNA hybrid molecules.