Peptide Barcodes for Protein Detection via Nucleic Acid Sequencing
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Solution Overview
Problem
Current methods for assessing binding agents, particularly proteins, in complex environments are slow, costly, and limited in throughput, with DNA barcoding technologies facing issues of stability and immunogenicity, and existing protein measurement techniques restricted by visible light wavelength constraints.
Innovation Solution
The use of peptide barcodes and nucleic acid sequencing technologies to accurately detect and quantify multiple protein agents in complex systems without direct covalent association with DNA, employing engineered barcode sequences and binders with known specificities and affinities to achieve high-throughput and precise measurement.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If DNA barcoding technologies are used to assess protein agents, then measurement throughput is improved, but stability and immunogenicity problems occur
Solution Approach 1:
The invention separates the detection system into two independent components: peptide barcodes that tag the protein agents and nucleic acid-based binders that detect the barcodes. This segmentation allows the protein assessment function while eliminating the need for covalent DNA-protein conjugation, thereby resolving the stability issues associated with DNA barcodes.
Solution Approach 2:
The invention introduces peptide barcodes as intermediary tags that can be stably incorporated into proteins and detected by nucleic acid-based binders. This intermediary system enables high-throughput measurement without directly attaching unstable DNA barcodes to proteins, thus maintaining both productivity and reliability.
2Measurement precision
If mass spectroscopy and affinity detection are used to assess binding agents, then measurement accuracy is improved, but assessment speed and cost increase
Solution Approach 1:
The invention merges the specificity of affinity detection with the high-throughput capabilities of nucleic acid sequencing. By using nucleic acid-based binders that specifically recognize peptide barcodes and leveraging next-generation sequencing technology, the system achieves both high measurement precision and rapid parallel assessment of multiple protein agents.
Solution Approach 2:
The nucleic acid-based binder system serves multiple functions: it provides specific recognition of target proteins through peptide barcode binding, enables amplification of detection signals, and allows parallel sequencing-based quantification. This multi-functionality simultaneously improves detection accuracy and assessment throughput.
3Ease of operation
If visible light wavelength detection is used for protein measurement, then detection simplicity is improved, but measurement multiplexing capability deteriorates
Solution Approach 1:
The invention replaces optical detection methods with nucleic acid-based detection and sequencing technology. Instead of using visible light wavelengths that are limited in multiplexing capability, the system uses nucleic acid binders and sequencing, which can simultaneously distinguish and quantify numerous different peptide barcodes through sequence variation, thereby achieving high multiplexing while maintaining operational simplicity.
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 accurate and efficient detection and measurement of multiple protein agents in complex systems, overcoming limitations of existing technologies by allowing simultaneous measurement of multiple proteins and providing precise quantification without altering protein functionality.
Implementation Method 1
employing engineered barcode sequences and binders with known specificities and affinities
Implementation Method 2
The relative amounts of each binder present in a sample are determined, for example, by amplifying and/or sequencing the nucleic acid of the population of binding agents
Data Source
AI summary
Methods and systems for quantification of an abundance of one or more payloads (e.g. proteins) in a mixture (e.g. a complex mixture (e.g. in vivo)) using barcodes (e.g. peptide barcodes), binders (e.g. polypeptide binders), and binding agents (e.g. phage) are provided herein.