Aptamer ID Sequencing for Scalable Protein Quantification
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Solution Overview
Problem
Current methods for quantifying proteins using SOMAmer reagents, such as microarray hybridization, face limitations in scalability and fixed assay costs, and there is a lack of commercial sources for microarrays, necessitating the development of alternative methods for quantifying SOMAmer molecules in a post-capture eluate.
Innovation Solution
The use of hybridization-capture (HC) techniques where SOMAmer eluate molecules are replaced by 'reporter' DNA molecules containing SOMAmer-specific identification tags, which are then sequenced using next-generation sequencing (NGS) technology to quantify protein abundances.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If microarray hybridization is used to quantify SOMAmer molecules, then protein detection can be achieved, but scalability is limited and assay costs are fixed
Solution Approach 1:
The patent uses next-generation sequencing to create digital copies and counts of SOMAmer molecules through DNA sequencing reads. Each SOMAmer molecule is converted into a sequencable DNA tag, allowing parallel processing and quantification of thousands of proteins simultaneously, thereby achieving both precision and scalability
Solution Approach 2:
The patent replaces the mechanical microarray hybridization system with a biochemical sequencing system. Instead of relying on physical microarray chips and hybridization kinetics, the invention uses DNA tag sequencing with bioinformatic analysis, enabling scalable and flexible protein quantification without the constraints of fixed microarray designs
2Measurement precision
If microarray hybridization is used to quantify SOMAmer molecules, then protein detection can be achieved, but commercial sources for microarrays are limited
Solution Approach 1:
The patent creates a universal sequencing-based platform that can quantify any SOMAmer molecule through a common DNA tag sequencing workflow. This universal approach replaces the need for custom microarray designs for different protein panels, allowing the same sequencing infrastructure to serve multiple applications and enhancing both adaptability and versatility
Solution Approach 2:
The invention uses DNA copy tags that can be universally amplified and sequenced using standard NGS protocols. This copying mechanism allows any SOMAmer probe set to be quantified through the same sequencing workflow, providing flexibility to adapt to different protein targets without requiring new commercial microarray products
3Measurement precision
If SOMAmer eluate molecules are directly sequenced, then protein quantification is possible, but the aptamers themselves are difficult to sequence
Solution Approach 1:
The patent introduces DNA tag molecules as intermediaries that bridge SOMAmer molecules and the sequencing instrument. These tags hybridize to SOMAmers, are captured and amplified, and then sequenced instead of the SOMAmer sequences themselves. This intermediary approach converts the difficult-to-sequence aptamers into easily sequenced DNA tags, solving the technical barrier while preserving quantification accuracy
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 scalable and cost-effective quantification of proteins by leveraging NGS technology, overcoming the limitations of microarray hybridization and providing accurate protein abundance measurements.
Implementation Method 1
capturing target proteins by exposing a biological sample to a plurality of aptamers
Implementation Method 2
forming a plurality of tri-molecular complexes by exposing the aptamers in the eluate to a plurality of capture probes each configured to hybridize to a particular aptamer
Implementation Method 3
sequencing the aptamer ID sequences via next-generation sequencing
Data Source
AI summary
Methods of detecting and quantifying target molecules, such as proteins, in a biological sample are provided. The disclosed methods include capturing target molecules with aptamers, replacing the aptamers with aptamer identification sequences, and then sequencing the aptamer identification sequences using next-generation sequencing techniques.