DNA Barcoded Affinity Reagents for Multiplexed Protein Quantification
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Solution Overview
Problem
Current methods for high-throughput measurement of proteins are limited by low throughput and difficulty in multiplexed detection, particularly in reflecting the current state of biology, as they lack a protein equivalent to DNA base pairing and struggle with simultaneous measurement of multiple proteins and their post-translational forms.
Innovation Solution
The use of modified affinity reagents, such as antibodies or aptamers, with unique DNA barcodes flanked by amplifying sequences, allowing for high-throughput target molecule identification and quantification through binding, amplification, and sequencing, enabling simultaneous measurement of multiple targets in a single sample.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If mass spectrometry is used to detect proteins, then nearly universal protein detection capability is achieved, but throughput is very low and analysis time is long
Solution Approach 1:
The patent creates DNA copy versions of proteins (proteobarcodes) that can be amplified and sequenced. Instead of directly analyzing proteins through low-throughput mass spectrometry, the invention synthesizes DNA copies that represent the proteome, enabling high-throughput sequencing-based analysis that maintains universal detection capability while dramatically increasing productivity
Solution Approach 2:
The patent replaces the mechanical/physical separation and detection system of mass spectrometry with a biochemical amplification and sequencing system. By substituting the detection mechanism from mass spec to DNA sequencing with PCR amplification, the system achieves both universal protein detection and high throughput
2Measurement precision
If traditional antibody-based methods are used to measure proteins, then specific target detection is achieved, but simultaneous multiplexed measurement of multiple proteins is difficult
Solution Approach 1:
The patent creates a universal DNA-based system (proteobarcodes) that can simultaneously represent multiple different proteins through unique DNA sequences. Each protein target is represented by a specific DNA barcode, allowing hundreds or thousands of proteins to be measured in a single sequencing run while maintaining the specificity of individual target detection through unique sequence identification
Solution Approach 2:
The invention creates DNA copy representations of multiple proteins simultaneously. Instead of using multiple different antibodies requiring separate assays, the system synthesizes DNA copies of multiple protein targets that can all be amplified and detected in a single high-throughput sequencing experiment, enabling easy multiplexing
3Productivity
If genome measurements are performed to assess gene expression, then global scale analysis is achieved, but the genome does not always reflect the actual state of biology
Solution Approach 1:
The patent performs preliminary synthesis of DNA copies (proteobarcodes) that directly represent the proteome rather than inferring protein levels from genomic DNA. By creating DNA representations that mirror actual protein presence and modification states before analysis, the system ensures the measurements reflect the true biological state rather than just genomic potential
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 enables efficient, multiplexed detection and quantification of proteins and their forms, providing a more accurate reflection of biological states by using DNA barcodes linked to affinity reagents, which can be amplified and sequenced for precise measurement.
Implementation Method 1
affinity reagents, each having affinity for a particular target molecule
Implementation Method 2
each identifying nucleotide sequence is flanked by a first amplifying nucleotide sequence and a second amplifying nucleotide sequence
Data Source
AI summary
Provided herein are affinity reagents having affinity for particular target, each reagent having a unique DNA barcode, and methods for using the same to measure the abundance of targets in a sample. In particular, methods are provided in which unique barcodes linked to affinity reagents are contacted to a sample to bind antigens if present in said sample. In cases in which the affinity reagents are antibodies and the targets are antigens, antibodies that are bound to their target antigens can be separated from unbound antibodies and the DNA barcode associated with the affinity reagent is amplified, such as with a PCR reaction. In some cases, amplified barcode DNA is subjected to DNA sequencing as a measure of the levels of the target protein in the sample.