Fluorinated Carbon Tagged Hybridization Probes for Nucleic Acid Purification
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Solution Overview
Problem
Current nucleic acid hybridization probes face challenges in purification during production and in the isolation and enrichment of their complexes with target nucleic acids from complex nucleic acid samples.
Innovation Solution
Development of hybridization probes with fluorinated carbon tags (FT) that facilitate affinity capture using fluorous substrates, enabling efficient purification and enrichment of target nucleic acids.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If biotinylated hybridization probes are used for capturing target nucleic acids, then enrichment capability is improved, but purification difficulty increases
Solution Approach 1:
The probe is divided into two independent affinity tags: biotin for capture and fluorinated carbon chain for purification. This segmentation allows each tag to perform its specific function without interfering with the other, resolving the contradiction between enrichment capability and purification difficulty
Solution Approach 2:
The fluorinated carbon chain acts as an intermediary between the probe and fluorous substrates, enabling selective purification through fluorous interaction while the biotin tag maintains the capture function. This intermediary element solves the purification problem without compromising enrichment capability
2Reliability
If conventional hybridization probes are used, then detection is possible, but selectivity and sensitivity are insufficient
Solution Approach 1:
The introduction of fluorinated carbon chains changes the physical-chemical parameters of the probe, enabling fluorous interaction-based purification that significantly enhances selectivity and sensitivity. This parameter change allows differentiation between target and non-target nucleic acids with high precision
Solution Approach 2:
The probe combines conventional nucleic acid sequences with fluorinated carbon chain materials to create a composite structure. This composite material leverages both the sequence-specific binding of DNA/RNA and the selective fluorous interaction, achieving superior selectivity and sensitivity in detection
3Productivity
If fluorinated carbon tags are introduced to improve purification, then purification efficiency is improved, but probe structure complexity increases
Solution Approach 1:
The fluorinated carbon chain serves as a simplified copy of the purification function, providing a direct fluorous interaction mechanism that is easier to implement than conventional purification methods. This copying approach improves purification efficiency while maintaining relatively simple probe structure
Solution Approach 2:
The fluorinated carbon chain provides multi-functionality: it enables purification during production, facilitates isolation from complex samples, and maintains probe stability. This universal element achieves multiple objectives without proportionally increasing structural 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 use of FT-tagged hybridization probes enhances the purification and enrichment processes, improving the selectivity and sensitivity of nucleic acid detection and analysis.
Implementation Method 1
hybridization probes that contain fluorinated carbon chains to facilitate their purification using fluorous substrates during production and to facilitate the isolation and enrichment of their complexes with target nucleic acids from complex nucleic acid samples
Data Source
AI summary
In one aspect, disclosed herein are new hybridization probes that contain fluorinated carbon tags (F), methods of making these hybridization probes, and methods for using these hybridization probes for affinity capture of the probes both in purification during production and in the enrichment process using fluorous substrates. In certain embodiments, the hybridization probe comprises a) a polynucleotide having a 3′ end and a 5′ end and comprising about 20 to about 200 nucleotide units and b) one or more fluorinated affinity tags, wherein each affinity tag comprises one or more polyfluorinated carbon chains each comprising 3-30 carbon atoms; wherein the polynucleotide comprises a sequence complementary or substantially complementary to a target sequence within a target nucleic acid.