Duplex Nucleic Acid Labels to Prevent Fluorescent Dye Self-Quenching
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Solution Overview
Problem
The incorporation of numerous individual dyes in markers leads to self-quenching, reducing fluorescence intensity and complicating quantitative analysis, especially in high-resolution studies.
Innovation Solution
A label comprising a nucleic acid backbone with a duplex structure and a plurality of labelling moieties, such as fluorescent dyes, is used to maintain rigidity and spacing, preventing dye aggregation and enhancing emission efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If numerous individual dyes are incorporated in markers, then sensitivity and detection capability are improved, but self-quenching occurs reducing fluorescence intensity
Solution Approach 1:
A rigidifying agent is introduced as an intermediary substance that mediates between the dyes and the polymer backbone. This agent forms rigidifying structures that spatially separate the dyes while maintaining their attachment to the polymer, thereby preventing self-quenching and preserving fluorescence intensity even when multiple dyes are incorporated.
Solution Approach 2:
The physical state and spatial arrangement of dyes are changed by introducing rigidifying structures. This alters the distance and orientation parameters between adjacent dyes, preventing the close proximity that causes self-quenching while maintaining the high dye loading necessary for sensitive detection.
2Measurement precision
If numerous individual dyes are incorporated in markers, then detection capability is improved, but quantitative analysis becomes complicated
Solution Approach 1:
The rigidifying agent serves as a standardized intermediary that provides consistent spatial separation and rigidification. This standardization ensures uniform optical properties across different markers, simplifying quantitative analysis by reducing variability in fluorescence intensity that would otherwise complicate measurements.
Solution Approach 2:
By controlling and standardizing the spatial arrangement parameters of dyes through rigidifying structures, the optical properties become predictable and consistent. This allows for simplified quantitative analysis as the relationship between dye concentration and fluorescence signal becomes more reliable.
3Illumination intensity
If numerous individual dyes are incorporated in markers, then brightness is improved, but self-quenching reduces emission efficiency
Solution Approach 1:
The rigidifying agent acts as a mediator that enables high dye loading for brightness while preventing the energy loss associated with self-quenching. By creating rigid structures that maintain optimal spacing, it allows multiple dyes to contribute to brightness without the harmful energy transfer between adjacent dyes.
Solution Approach 2:
The spatial parameters between dyes are optimized through rigidifying structures, maintaining distances that prevent self-quenching while allowing sufficient dye density for high brightness. This parameter control ensures that emission efficiency is preserved even as total fluorescence intensity increases through multiple dyes.
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 nucleic acid backbone with a duplex structure maintains the native optical properties of labelling moieties, providing bright and efficient emission, thereby improving sensitivity and accuracy in biological analysis.
Implementation Method 1
The nucleic acid backbone has a duplex structure comprising at least 50% of nucleotides of the nucleic acid backbone
Implementation Method 2
The nucleic acid backbone is configured to allow formation of a duplex structure
Implementation Method 3
Self-quenching occurs when the proximity of dyes within a marker leads to non-radiative energy transfer among them, significantly diminishing the emission efficiency and the fluorescence intensity
Data Source
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AI summary
A label (100, 200, 500, 702, 802, 900, 901, 1000, 1200, 1300, 1600) for analysing a biological sample is provided. The label (100, 200, 500, 702, 802, 900, 901, 1000, 1200, 1300, 1600) comprises a nucleic acid backbone (102, 502, 1002, 1102, 1202, 1301) and a first plurality of labelling moieties (104). The nucleic acid backbone (102, 502, 1002, 1102, 1202, 1301) has a duplex structure comprising at least 50% of nucleotides of the nucleic acid backbone (102, 502, 1002, 1102, 1202, 1301). In further aspects a marker (700, 800) comprising the label and a method for analysing biological samples is provided.