Aptamer-Based Protein Sequencing Platform for High-Throughput Analysis
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Solution Overview
Problem
Current methods for protein sequencing are not cost-effective or high-throughput, and they struggle to sequence untargeted lowly expressed proteins, making it difficult to access information about protein levels and their enzymatic effects, especially for antibodies and proteins in complex samples.
Innovation Solution
A protein sequencing platform using aptamers that bind specifically to N-terminal amino acids, generated through novel methods like RCHT-SELEX, which allows for the recognition and conversion of amino acids into DNA sequences, enabling the sequencing of proteins and peptides in a high-throughput manner by ligating DNA aptamers to peptides and removing amino acids for sequential barcode construction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional protein sequencing methods are used, then sequencing capability is limited, but cost and time requirements become prohibitive for large-scale applications
Solution Approach 1:
The protein sequencing process is segmented into discrete cycles: amino acid removal, aptamer binding, barcode ligation, and sequencing. Each cycle processes one amino acid position, enabling systematic high-throughput sequencing of entire proteins by breaking down the complex task into manageable, automatable steps
Solution Approach 2:
DNA aptamers serve as intermediary molecules that bind specifically to N-terminal amino acids and carry unique barcodes. These aptamers mediate the conversion of protein sequence information into readable DNA barcode sequences, enabling the sequencing process to leverage efficient DNA handling and sequencing technologies
2Adaptability or versatility
If conventional sequencing methods are used, then existing protein information can be accessed, but untargeted lowly expressed proteins remain inaccessible
Solution Approach 1:
The aptamer-based sequencing platform provides universal applicability across all protein types, including untargeted and lowly expressed proteins. The method does not require prior knowledge of target sequences or enrichment steps, enabling direct sequencing of any protein in the sample with consistent accuracy regardless of abundance
3Loss of information
If comprehensive protein information is obtained, then correlations between protein levels and enzymatic effects can be inferred, but current methods lack the throughput for extensive physiological monitoring
Solution Approach 1:
The patent replaces traditional mechanical/protein-based detection methods with a nucleic acid-based system. By converting protein sequence information into DNA barcode sequences through aptamer binding and ligation, the system leverages the efficiency, automation capability, and high throughput of DNA sequencing technologies to achieve comprehensive protein information at scale
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, high-throughput sequencing of proteins and peptides, including lowly expressed ones, allowing for the identification of biomarkers and evaluation of disease states by converting protein sequences into readable DNA signals, thereby overcoming the limitations of existing technologies.
Implementation Method 1
incubating the peptide with a library of DNA aptamers exhibiting binding specificity toward at least one N-terminal amino acid under conditions where one or more aptamers bind specifically to at least one N-terminal amino acid of the peptide
Data Source
AI summary
This disclosure describes methods and compositions for protein and peptide sequencing.