Barcode Molecule Substrate for Single-Particle Analyte Detection
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Solution Overview
Problem
Current methods struggle to effectively detect and quantify analytes in single biological particles, such as single cells or nuclei, as they provide limited insights into the specific analytes related to the binding events and substances involved.
Innovation Solution
A system is developed that includes a substrate with biological particle capture moieties and barcode molecules, where analytes from captured biological particles are analyzed using barcode molecules to identify specific analytes related to the binding event, minimizing diffusion and allowing for the detection and quantification of analytes on a single-particle basis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If single biological particle detection methods are used, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The substrate is divided into multiple discrete capture regions, each containing a biological particle capture moiety and associated barcode molecules. This segmentation allows independent analysis of analytes from individual biological particles while maintaining a manageable overall system structure that can be manufactured and operated effectively.
Solution Approach 2:
Barcode molecules serve as intermediaries between the biological particle capture moieties and the analytes. These barcodes enable the linkage of spatial information (capture region location) with molecular identity (analyte type), simplifying the detection process by providing a readable code that identifies both the particle source and the analyte without requiring complex direct detection mechanisms.
2Measurement precision
If barcode molecules are associated with capture moieties to identify specific analytes, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The barcode molecules perform multiple functions: they serve as identifiers for capture regions, enable analyte binding through complementary sequences, and provide spatial mapping information. This multi-functionality reduces the need for separate molecular components, thereby managing complexity while achieving precise analyte identification.
Solution Approach 2:
The system utilizes sequence complementarity as a key parameter to achieve specific binding between barcode molecules and analytes. By changing the nucleotide sequence parameters of the barcode molecules, the system can selectively bind to different analytes from the same biological particle, enabling precise identification without adding complex mechanical or optical systems.
3Measurement precision
If diffusion of analytes is limited to associated barcode molecules, then measurement precision is improved, but device complexity increases
Solution Approach 1:
Each capture region on the substrate is designed with local quality - the barcode molecules are positioned and oriented specifically to receive analytes from the adjacent biological particle capture moiety. This localized arrangement ensures that analytes remain bound to their originating particle's associated barcodes, enabling precise localization without requiring complex physical barriers or additional structural elements.
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 system enables the detection and analysis of specific analytes from single biological particles, correlating binding events with the molecules involved, providing detailed information about the biological particles.
Implementation Method 1
The barcode molecules may include a common barcode sequence and an analyte binding sequence... capable of hybridizing to analytes from the biological particles
Implementation Method 2
capable of hybridizing to analytes from the biological particles (e.g., RNAs) having complementary nucleotide sequences
Implementation Method 3
The binding may be specific in that, in some examples, biological particles may have a receptor that binds to a ligand that is part of the biological particle binding moiety
Data Source
AI summary
Disclosed are systems and methods for selecting biological particles (e.g., cells or nuclei) based on specific binding to a substrate and single-biological particle measurement of analytes from the substrate-bound biological particles (e.g., cells or nuclei). Single biological particles (e.g., cells or nuclei) from a population of biological particles are captured through their binding to biological particle-(e.g., cell- or nucleus-) and/or molecule-specific biological particle (e.g., cell or nucleus) capture moieties on a substrate. Analytes are released from the single captured biological particles (e.g., cells or nuclei) and bind to analyte-specific barcode molecules associated with the specific biological particle (e.g., cell or nucleus) capture moieties to which a biological particle (e.g., a cell or nucleus) has bound. Analysis of the barcode molecules identifies the bound analytes. The systems and methods are used to select and capture immune cells, such as T-cells that bind specific peptide epitopes through their T-cell receptors (TCRs) or B-cells that bind antigen through their B cell receptors (BCRs). Detection and analysis of barcode molecules that have bound cellular analytes comprising rearranged V(D)J-expressing RNAs from the T-cells or B-cells allows identification of the specific TCR sequences that recognize and bind the specific peptide epitopes or specific BCR sequences that recognize and bind specific antigens.