DNA-Linked Biomarker Profiling for High-Multiplex Single-Cell Detection
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Solution Overview
Problem
Conventional biomedical techniques struggle to simultaneously analyze a large number of biomarkers at the single-cell level due to limitations in multiplexing capabilities, leading to incomplete understanding of disease processes and diagnostic challenges.
Innovation Solution
A hybrid immunofluorescence and fluorescence in situ hybridization (IF/FISH) method using quantum dot probes, where each biomarker is encoded with a unique DNA tag, allowing for multiplexed detection and quantification through reversible conjugation and sequential staining cycles.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If conventional biomedical techniques are used for biomarker analysis, then the analysis process is simple, but the number of biomarkers that can be analyzed simultaneously is limited
Solution Approach 1:
The patent divides the detection system into distinct segments: quantum dot probes with unique DNA tags for each biomarker, affinity molecules for specific binding, and fluorescent labels for detection. This segmentation allows multiple biomarkers to be analyzed simultaneously while maintaining system manageability through modular components.
Solution Approach 2:
The patent employs universal quantum dot probes that can bind to multiple different affinity molecules through DNA hybridization. Each quantum dot probe contains a universal binding domain that interacts with various affinity molecules, enabling a single probe type to detect multiple biomarkers through sequential staining cycles, thus achieving multi-functionality.
2Quantity of substance
If conventional immunohistochemical staining is used, then the staining process is straightforward, but the multiplexing capability is limited to a small number of biomarkers
Solution Approach 1:
The patent implements periodic action through sequential staining cycles where quantum dot probes are repeatedly applied and removed in cycles. Each cycle detects a subset of biomarkers, and by repeating the process with different probe sets, comprehensive multiplexed detection is achieved. This periodic approach enables high multiplexing capability while maintaining operational feasibility through standardized repetitive steps.
3Loss of information
If quantum dot probes with unique DNA tags are used for each biomarker, then comprehensive molecular profiling is enabled, but the complexity of probe design and implementation increases
Solution Approach 1:
The patent introduces DNA tags as intermediary elements that bridge the quantum dot probes and affinity molecules. Each biomarker is associated with a unique DNA tag on the quantum dot probe, which hybridizes to a complementary DNA sequence on the affinity molecule. This intermediary DNA-based recognition system enables comprehensive molecular profiling through sequence-specific binding while simplifying probe design through the use of programmable DNA sequences rather than complex protein-protein interactions.
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
Enables comprehensive molecular profiling of cells with high multiplexing capability, overcoming limitations of conventional methods by uniquely assigning biomarkers to fluorescent probes, facilitating accurate diagnostics and therapeutic targeting.
Implementation Method 1
quantum dot probes, where each biomarker is encoded with a unique DNA tag, allowing for multiplexed detection and quantification through reversible conjugation and sequential staining cycles
Implementation Method 2
each biomarker is encoded with a unique DNA tag, allowing for multiplexed detection and quantification through reversible conjugation
Data Source
AI summary
Provided herein are compositions and methods for identifying or quantitating one or more analytes in sample. The composition can comprise an affinity molecule reversibly conjugated to a label moiety via a double-stranded nucleic acid linker or via an adaptor molecule. The affinity molecule and the label moiety can be linked to different strands of the double-stranded nucleic acid linker. Compositions can be used in any biological assays for detection, identification and/or quantification of target molecules or analytes, including multiplex staining for molecular profiling of individual cells or cellular populations. For example, the compositions can be adapted for use in immunofluorescence, fluorescence in situ hybridization, immunohistochemistry, western blot, and the like.