Aptamer Barcoding for Quantitative Protein and Gene Expression
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Solution Overview
Problem
Current technologies are limited in their ability to quantitatively analyze protein expression in cells and simultaneously measure protein and gene expression in a manner that allows for accurate identification of sample origins and protein targets.
Innovation Solution
A method utilizing aptamers and sample indexing oligonucleotides to specifically bind to protein targets, followed by barcoding and sequencing to identify sample origins and quantify protein expression, incorporating aptamer compositions and sample indexing sequences to generate barcoded oligonucleotides for sequencing data analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If molecular barcoding techniques are used to measure gene expression in single cells, then measurement capability is improved, but the ability to quantitatively analyze protein expression and simultaneously measure both protein and gene expression remains insufficient
Solution Approach 1:
The patent combines protein detection (via aptamers) and gene expression detection (via mRNA barcoding) into a single integrated workflow. Both protein targets and poly(A) mRNA molecules are labeled with barcodes in the same reaction mixture, allowing simultaneous measurement of both proteome and transcriptome from the same single cells, thereby resolving the contradiction between measurement precision and analytical versatility
Solution Approach 2:
The patent employs a universal barcode structure that serves multiple functions: it identifies protein targets through aptamer binding, tracks gene expression through mRNA association, and enables sample multiplexing through unique molecular identifiers. This multi-functional barcode system allows a single method to perform both protein and gene expression analysis, addressing the versatility limitation
2Reliability
If sample indexing compositions are used to identify sample origins, then sample identification capability is improved, but the precision of identifying both sample origin and protein target simultaneously is insufficient
Solution Approach 1:
The barcode structure is segmented into distinct functional regions: a sample indexing sequence for identifying sample origin, a target-specific sequence for identifying protein targets, and a unique molecular identifier for tracking individual molecules. This segmentation allows each component to be independently optimized and accurately read, enabling simultaneous precise identification of both sample origin and protein target without cross-interference
Solution Approach 2:
The aptamer serves as an intermediary that bridges protein target detection and barcode labeling. The aptamer specifically binds to the protein target and is conjugated to the barcode, ensuring that the barcode is accurately associated with the correct protein target while the sample indexing sequence on the same barcode accurately identifies the sample origin, thereby maintaining precision in simultaneous identification
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 the quantitative analysis of protein expression and simultaneous measurement of gene expression, allowing for accurate identification of sample origins and protein targets through sequencing data, enhancing the precision of molecular barcoding techniques.
Implementation Method 1
the aptamer is capable of specifically binding to at least one of the one or more protein targets
Data Source
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AI summary
Disclosed herein include systems, methods, compositions, and kits for sample identification and protein expression profiling. A sample indexing composition, or a composition for protein expression profiling, can comprise, for example, a protein binding aptamer associated with an oligonucleotide, such as a sample indexing oligonucleotide. Different oligonucleotides can have different sequences. Sample origin of cells, or protein expression profiles of cells, can be determined based on the sequences of the oligonucleotides by, for example, barcoding the oligonucleotides.