Blocking Nucleic Acid Labels for Specific Proximity Detection
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Solution Overview
Problem
Existing biological sample analysis methods face challenges with cross-reactivity of affinity reagents, leading to false-positive results and reduced specificity, especially in high-plexity applications like cytometry and microscopy, which are costly and affect reproducibility in life science research.
Innovation Solution
A label comprising a first and second nucleic acid strand with labelling moieties and a blocking nucleic acid strand, allowing controlled duplex formation only when affinity reagents are in close proximity, using enzymatic or chemical means to remove the blocking strand and enable specific detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If affinity reagents are used for detecting analytes in biological samples, then detection capability is improved, but cross-reactivity occurs leading to false-positive results and reduced specificity
Solution Approach 1:
The detection system is segmented into multiple independent components: first affinity reagent, second affinity reagent, first label part, second label part, and blocking nucleic acid strands. Each component performs a specific function, and the system requires coordinated interaction of all segments to produce a valid signal, thereby reducing cross-reactivity while maintaining detection capability
Solution Approach 2:
Blocking nucleic acid strands act as intermediaries that prevent non-specific binding between affinity reagents and analytes. These blocking strands are removed under specific conditions to enable the actual detection reaction, thereby improving specificity while preserving the detection function of the affinity reagents
2Adaptability or versatility
If multiple affinity reagents and labels are used for multiplexing, then detection capacity is improved, but handling complexity increases
Solution Approach 1:
The label structure is designed with universal features that can be applied across multiple detection channels. The same basic label architecture with blocking nucleic acid strands can be used for different analytes and detection modes, reducing the need for entirely different reagent sets and simplifying handling while maintaining high detection capacity
Solution Approach 2:
Multiple functional elements are merged into a single integrated label structure that combines affinity reagents, labeling moieties, and blocking nucleic acid strands. This merging reduces the number of separate components that need to be handled and coordinated, thereby reducing handling complexity while maintaining multiplexing capability
3Reliability
If affinity reagents with high affinity are used, then binding specificity is improved, but cross-reactivity with similar analytes increases
Solution Approach 1:
The blocking nucleic acid strands are extracted and removed under specific detection conditions, separating the binding function (performed by affinity reagents) from the detection function (performed by labeling moieties). This extraction step eliminates cross-reactivity issues by ensuring that only properly paired affinity reagents and analytes produce detectable signals
Solution Approach 2:
The system incorporates feedback through the blocking nucleic acid strands that monitor and control the binding events. The blocking strands are removed only when proper binding occurs, providing feedback that confirms specific interactions and prevents false-positive results from cross-reactive binding events
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
Enhances assay specificity by mitigating cross-reactivity, enabling precise detection of analyte proximities and reducing false positives, particularly suitable for high-plexity applications like spatial interactomics and protein-protein interaction studies.
Implementation Method 1
The first nucleic acid strand and the second nucleic acid strand are configured to form a duplex
Implementation Method 2
The at least one blocking nucleic acid strand is at least partially complementary to one of the first nucleic acid strand and the second nucleic acid strand
Data Source
AI summary
A label for analyzing a biological sample includes a first label part comprising a first nucleic acid strand, and a second label part comprising a second nucleic acid strand. The first nucleic acid strand and the second nucleic acid strand are configured to form a duplex. The label further includes at least one first labelling moiety and at least one second labelling moiety, and at least one blocking nucleic acid strand. The at least one blocking nucleic acid strand is at least partially complementary to one of the first nucleic acid strand and the second nucleic acid strand.