Elemental Tag Oligonucleotide Probes for Single Cell Gene Expression
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Solution Overview
Problem
Current gene and protein expression analysis methods lack sensitivity and multiplexing capabilities, especially for single cells, leading to incomplete genomic information and interference from heterogeneous cell populations.
Innovation Solution
The use of elemental tags attached to oligonucleotide probes and microspheres for hybridization, followed by inductively coupled plasma mass spectrometry (ICP-MS) analysis, allows for sensitive and quantitative detection of multiple mRNA species in single cells without fluorescent labeling, enabling simultaneous analysis of gene and protein expression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If fluorescent labeling is used for gene expression analysis, then detection capability is improved, but sensitivity and multiplexing capabilities are limited
Solution Approach 1:
The patent changes the detection parameter from fluorescent labeling to elemental tags detectable by ICP-MS. This parameter change enables simultaneous detection of multiple mRNA species (multiplexing) with high sensitivity, as ICP-MS can distinguish between different elements and isotopes, allowing up to 70-plex detection compared to limited fluorescent channels
Solution Approach 2:
The patent replaces the optical detection system (fluorescence microscopy/flow cytometry) with a mass spectrometry-based detection system (ICP-MS). This substitution eliminates the limitations of fluorescent labeling by using elemental tags that can be detected with superior sensitivity and multiplexing capability, as mass spectrometry can simultaneously resolve multiple elemental signals without spectral overlap
2Ease of operation
If conventional gene expression methods are used, then analysis is simpler, but sensitivity for single cells is insufficient
Solution Approach 1:
The patent introduces elemental tags as intermediaries that attach to oligonucleotide probes for hybridization to target mRNA. These elemental tags serve as detectable mediators that amplify the signal from single cell mRNA, enabling sensitive detection by ICP-MS while maintaining the simplicity of hybridization-based analysis
Solution Approach 2:
The patent segments the detection approach by using multiple distinct elemental tags (different elements or isotopes) to label different probes targeting different mRNA species. This segmentation allows simultaneous analysis of multiple genes in single cells, with each element providing an independent detection channel that contributes to overall sensitivity
3Quantity of substance
If heterogeneous cell populations are analyzed, then sample representivity is improved, but genomic information completeness deteriorates due to interference
Solution Approach 1:
The patent replaces conventional detection methods with ICP-MS-based detection of elemental tags. This substitution provides superior signal-to-noise ratio and sensitivity, enabling clear distinction of hybridization signals from heterogeneous cell populations without interference, thus preserving complete genomic information even in mixed samples
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
This approach provides high sensitivity and accuracy in analyzing hundreds of thousands of mRNA molecules, improving detection efficiency and excluding fluorescent labeling, thus offering a robust and quantitative measurement of RNA levels in biological samples.
Implementation Method 1
hybridization of complementary oligonucleotides to target mRNA
Implementation Method 2
inductively coupled plasma mass spectrometry (ICP-MS) analysis
Implementation Method 3
elemental analysis by ICP-MS
Data Source
Figure 1A~1B
Figure 2A~2B
Figure 3
AI summary
Methods and kits for gene expression analysis are disclosed. The methods utilize element-tagged oligonucleotides as probes which are subsequently analyzed by elemental analysis. Also disclosed are methods and kits for the analysis of biological molecules using element labeled supports such as beads, followed by elemental analysis. The elemental analysis can be done using inductively coupled plasma mass spectrometry (ICP-MS).