DNA-Encoded Probes for Proteomic Activity Analysis
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Solution Overview
Problem
Current methods for assessing proteomic information are costly, require specialized equipment, and lack the ability to provide accurate global profiles of enzymatic activity and small molecule activity, limiting their usefulness in diagnostic and screening assays.
Innovation Solution
A kit and method using DNA-encoded probes with amplifiable identification barcode regions linked to specific substrates, allowing for the detection of proteomic activity by quantifying changes in DNA constructs through PCR and sequencing, enabling low-cost, high-throughput analysis of enzymatic activity and ligand binding affinity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional methods (microfluidic devices, microarrays, mass spectrometry) are used for proteomic analysis, then measurement precision and sensitivity can be achieved, but device complexity and cost increase significantly
Solution Approach 1:
The patent uses DNA molecules as intermediary carriers to transfer proteomic information. Proteins are converted into DNA-encoded signals through proteomic mapping, where proteolytic digestion products are sequenced and mapped to DNA sequences. This DNA intermediary enables the use of simple, cost-effective DNA sequencing technology instead of complex proteomic instrumentation.
Solution Approach 2:
The patent replaces complex mechanical and instrumental systems (mass spectrometers, microfluidic devices, microarrays) with biochemical systems based on DNA manipulation. The detection mechanism shifts from physical measurement instruments to biochemical amplification and sequencing processes, which are simpler and more cost-effective.
2Loss of information
If conventional proteomic methods are used, then some proteomic information can be obtained, but the ability to provide accurate global profiles of enzymatic activity is limited
Solution Approach 1:
The patent segments the proteome into individual proteins and further segments each protein into proteolytic digestion products. Each peptide segment is then mapped to a specific DNA sequence segment, creating a hierarchical segmentation that enables comprehensive yet manageable proteomic analysis. This segmentation allows global profiling of enzymatic activities by tracking changes in specific peptide segments.
Solution Approach 2:
The patent creates a universal DNA-based coding system that can represent any protein in the proteome. The same DNA sequencing and analysis methodology can be applied universally across different proteins and different enzymatic activities, providing a multi-functional platform for comprehensive proteomic analysis including enzymatic activity profiling.
3Productivity
If DNA-encoded probes with PCR amplification are used, then sensitivity and multiplexing capabilities improve, but manufacturing complexity increases
Solution Approach 1:
The patent changes the detection parameter from direct protein measurement to DNA sequence measurement. By converting proteomic information into DNA sequences that can be amplified by PCR and analyzed by sequencing, the system achieves high multiplexing capability. The DNA parameters (sequence, length, amplification efficiency) are optimized to enable straightforward manufacturing and analysis.
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, cost-effective, and high-throughput profiling of proteomic activity, providing comprehensive information on enzymatic function and small molecule interactions, overcoming the limitations of existing technologies.
Implementation Method 1
the target protein capable of reacting with or binding the substrate of a probe to convert the substrate into a product
Implementation Method 2
the DNA construct comprising one or more amplifiable identification barcode regions... the attached marker DNA is then amplified by PCR
Data Source
AI summary
Systems, kits, and methods for detecting and quantifying proteomic activity using DNA-encoded probes are provided, where the proteomic activity may be enzymatic activity or ligand binding affinity. Such systems and methods encode quantitative proteomic activity information into DNA sequence populations and utilize DNA-linked substrates or ligands as activity probes. The systems, kits, and methods that are directed to detecting ligand affinity further include crosslinking steps to ensure the integrity of the DNA-linked ligands during purification and washing. Signal detection involves the chemical manipulation of a probe population downstream of sample exposure and application of purifying, selective pressure for desired products. Selection-induced changes in DNA abundance between the initial pool and the purified pool indicate sample activity.