Aptamer-Based Protein Sequencing Platform for High-Throughput Analysis
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for protein sequencing are not cost-effective or efficient for large-scale, high-throughput sequencing, and fail to robustly 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 and NTAA-SELEX, which convert amino acids into DNA sequences or provide visual signals, enabling simultaneous identification and sequencing of multiple targets with high specificity and affinity, utilizing nucleic acid barcodes and machine learning for optimization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional protein sequencing methods are used, then sequencing can be performed, but the process is not cost-effective and inefficient for large-scale, high-throughput sequencing
Solution Approach 1:
The patent replaces conventional mechanical/chemical sequencing methods with a molecular recognition system using aptamers. Aptamers are nucleic acid molecules that specifically bind to target amino acids, enabling parallel processing of multiple samples simultaneously. This substitution of mechanical sequencing with molecular recognition dramatically increases throughput while reducing per-sample costs through high-throughput screening capabilities.
Solution Approach 2:
The patent segments the protein sequencing process into discrete amino acid identification steps using specific aptamer-probe combinations. Each amino acid can be targeted independently with its own aptamer, allowing parallel sequencing of multiple proteins or multiple regions of the same protein. This segmentation enables high-throughput processing by breaking down the complex sequencing task into manageable, parallelizable units.
2Reliability
If conventional sequencing methods are used, then protein sequencing is possible, but untargeted lowly expressed proteins cannot be robustly sequenced
Solution Approach 1:
The patent introduces aptamers as intermediary molecules that mediate between the protein target and the detection system. These aptamers act as highly sensitive detectors that can identify even trace amounts of lowly expressed proteins. The aptamer-protein complex can then be enriched and amplified, making it possible to detect and sequence proteins that would be undetectable by conventional methods. This intermediary approach bridges the gap between low-abundance targets and detection capabilities.
Solution Approach 2:
The patent performs preliminary enrichment and selection of target proteins using aptamer-based affinity capture before sequencing. By pre-concentrating lowly expressed proteins through specific aptamer binding, the method ensures sufficient material is available for subsequent sequencing steps. This preliminary action of enrichment before detection makes the overall process robust for analyzing low-abundance proteins that would otherwise be lost in the noise.
3Measurement precision
If high specificity aptamer binding is achieved, then accurate amino acid identification is possible, but the complexity of generating and screening aptamer libraries increases
Solution Approach 1:
The patent employs self-service mechanisms where the aptamer library performs its own selection and enrichment. Through systematic evolution of ligands by exponential enrichment (SELEX), the library autonomously identifies and enriches for high-affinity binders to specific amino acids. The system uses its own diversity as a resource, with each round of selection automatically enriching for better binders without requiring external intervention to design individual aptamers. This self-organizing property reduces the complexity burden on researchers.
Solution Approach 2:
The patent systematically varies parameters during aptamer library development, including nucleotide composition, library diversity, and selection conditions, to optimize binding specificity. By controlling these parameters during library generation and screening, the method achieves high measurement precision for amino acid identification. The systematic parameter optimization ensures that aptamers with the desired specificity and affinity are selected while managing the complexity of the overall process.
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 allows for efficient, high-throughput sequencing of proteins and proteomes, including lowly expressed proteins, providing deeper insights into protein levels and enzymatic effects, and enabling the identification of novel proteins and biomarkers from small sample inputs.
Implementation Method 1
aptamers that bind specifically to N-terminal amino acids
Implementation Method 2
nucleic acid barcoded target generation can be accomplished in vivo via a non-covalent bond between a peptide or protein using an RNA-binding protein and its corresponding recognition sequence
Data Source
AI summary
This disclosure describes methods and compositions for protein and peptide sequencing.