Oligonucleotide Quencher Composition for Stable Aqueous Detection
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Solution Overview
Problem
Existing quenchers used in biology are limited by reactive groups that struggle with long-term stability and solubility, particularly in water-based conditions, and lack versatility in binding to various biomolecules effectively.
Innovation Solution
A novel quencher compound represented by Formula 1, which includes specific functional groups and linkers, allows for improved quenching efficiency and stability, enabling binding to a wide range of biomolecules through reactive groups like carboxyl, hydroxyl, and thiol groups, and is incorporated into oligonucleotides for nucleic acid detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional quenchers with standard reactive groups (succinimidyl ester, isothiocyanate, maleimide, dichlorotriazine) are used, then binding to biomolecules is achieved, but long-term reaction and storage stability under water-soluble conditions deteriorates
Solution Approach 1:
The patent modifies the chemical structure of the quencher by introducing a water-soluble sulfonate group and adjusting the reactive group to a stabilized form. These parameter changes in molecular structure enable the quencher to maintain both high reactivity for biomolecule binding and exceptional stability under water-soluble storage conditions, resolving the contradiction between reactivity and stability.
Solution Approach 2:
The quencher is designed as a composite structure combining a fluorescent dye moiety with a stabilized reactive group and water-solubilizing sulfonate groups. This composite design integrates multiple functional elements that work together to achieve both effective biomolecule binding and long-term stability in aqueous environments.
2Measurement precision
If fluorescent dyes are used for biomolecule detection, then detection capability is achieved, but quenching efficiency and signal-to-noise ratio deteriorate when conventional quenchers are employed
Solution Approach 1:
The stabilized quencher acts as an intermediary molecule that efficiently accepts energy from the fluorescent dye through FRET or electron transfer mechanisms. The optimized structure enables superior quenching performance, creating a more effective energy transfer pathway that enhances signal-to-noise ratio and detection sensitivity.
3Adaptability or versatility
If reactive groups are introduced to enable biomolecule binding, then binding versatility is achieved, but substitution reactions and long-term stability under water-soluble conditions deteriorate
Solution Approach 1:
The quencher molecule is designed with differentiated local properties: the reactive group region is optimized for specific biomolecule binding, while the sulfonate group regions provide water solubility and stability. This local quality differentiation allows the molecule to perform binding functions without compromising overall stability in aqueous storage conditions.
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 novel quencher exhibits enhanced quenching properties and stability, facilitating effective nucleic acid detection with improved sensitivity and specificity, overcoming limitations of conventional quenchers.
Implementation Method 1
A quenching phenomenon is known to occur through a mechanism including fluorescence resonance energy transfer (FRET), photo-induced electron transfer and dye coagulation such as H-dimer formation.
Implementation Method 2
A quenching phenomenon is known to occur through a mechanism including fluorescence resonance energy transfer (FRET), photo-induced electron transfer and dye coagulation such as H-dimer formation.
Data Source
AI summary
The present invention relates to an oligonucleotide comprising a quencher exhibiting a quenching effect on a fluorescent material exhibiting a luminescent property at an excited energy level, and various uses thereof.