Barcoded Nucleic Acid Encoding for Protein Identification
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Solution Overview
Problem
Current methods for high-throughput protein identification face challenges such as multiplexing affinity agents, minimizing cross-reactivity, and developing efficient read-out platforms, particularly in accurately identifying specific amino acid residues and their positions in polypeptides.
Innovation Solution
The use of barcoded nucleic acid tags to selectively label specific amino acid residues in polypeptides, allowing for cyclic encoding and decoding of information through nucleic acid sequencing, enabling the identification of polypeptides without protein-based or aptamer-based binding agents.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If affinity-based assays are used for high-throughput protein identification, then identification throughput is improved, but multiplexing affinity agents becomes difficult and cross-reactivity increases
Solution Approach 1:
The patent replaces affinity-based mechanical binding systems with nucleic acid encoding systems. Instead of using multiple affinity agents that require complex multiplexing and have cross-reactivity issues, the invention uses nucleic acid tags and barcodes that can be selectively encoded through chemical reactions. The identification process is substituted from physical binding assays to nucleic acid sequencing, enabling high-throughput parallel identification without the complexity of managing multiple affinity agents.
Solution Approach 2:
The patent introduces nucleic acid tags and barcodes as intermediary elements between the polypeptide and the detection system. These intermediaries carry encoding information that identifies specific amino acid residues or post-translational modifications. The intermediary nucleic acid sequences enable information transfer without requiring direct affinity binding, thus avoiding the multiplexing and cross-reactivity problems of traditional affinity-based systems.
2Measurement precision
If binding agents are used to identify amino acid residues, then identification accuracy is improved, but developing specific binders with strong affinity and specificity becomes challenging
Solution Approach 1:
The patent uses nucleic acid barcodes and tags as copies or representations of amino acid residue information. Instead of developing complex protein binders that directly recognize amino acids, the system creates simplified nucleic acid copies that encode residue identity. These nucleic acid barcodes can be easily synthesized and manipulated, avoiding the difficulty of evolving and characterizing specific protein binders while maintaining identification accuracy through the encoding information.
Solution Approach 2:
The patent changes the fundamental parameter of the identification system from protein-based binding affinity to nucleic acid-based encoding. By transforming the identification mechanism from measuring binding strength to reading encoded information, the system achieves high accuracy without the manufacturing challenges of developing specific binders. The nucleic acid sequences provide a standardized, easily manufacturable coding system that simplifies the development process.
3Productivity
If traditional protein identification methods are used, then method simplicity is maintained, but high-throughput parallel processing capability is limited
Solution Approach 1:
The patent segments the polypeptide identification process into discrete, parallelizable steps: (1) chemical labeling of amino acid residues with nucleic acid tags, (2) encoding of residue information into barcode sequences, (3) transfer of encoding information to recording tags, and (4) parallel sequencing of multiple polypeptides. This segmentation enables simultaneous processing of multiple samples through parallel nucleic acid sequencing, achieving high-throughput capability while keeping each individual step relatively simple and modular.
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 highly parallelized, accurate, and sensitive identification of polypeptides by leveraging the high affinity and specificity of nucleic acid tags, overcoming previous limitations in protein identification technologies.
Implementation Method 1
The use of barcoded nucleic acid tags to selectively label specific amino acid residues in polypeptides
Implementation Method 2
allowing for cyclic encoding and decoding of information through nucleic acid sequencing
Data Source
AI summary
The present disclosure relates to methods and kits for high-throughput, highly parallel polypeptide identification employing labeling of specific amino acid residues, barcoding and nucleic acid encoding of the labeled residues. The workflow and architecture described herein allow identification of polypeptides in a sample in a cyclic manner based on encoding of their specific amino acid residues and without use of protein-based or aptamer-based binding agents. Successful “binder-free” encoding takes advantage of the high affinity and specificity of nucleic acid tags, as well as the specific chemistry of certain amino acid side chains.