Antibody-DNA Adapter Barcoding for Multiplex Epigenetic Profiling
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Solution Overview
Problem
Current methods for detecting and quantifying multiple epigenetic modifications, such as protein-DNA interactions and histone modifications, in cells are limited to single modality measurements, requiring multiple assays and lacking reproducibility and efficiency.
Innovation Solution
A method utilizing antibody-DNA adapter conjugates for simultaneous assessment of multiple marks in cells, enabling high-throughput screening with single-cell resolution, using barcoding to identify and quantify interactions and modifications.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If multiple assays are performed to screen multiple parameters at single cell resolution, then measurement precision is improved, but device complexity and time consumption increase
Solution Approach 1:
The patent combines multiple ChIP-seq assays into a single multiplexed assay by using antibody-DNA adapter conjugates with unique barcodes for each antibody. This allows simultaneous detection of multiple protein-DNA interactions and histone modifications in the same cell, eliminating the need for separate assays while maintaining single-cell resolution measurement precision.
Solution Approach 2:
The patent creates a universal assay platform that can detect multiple different epigenetic marks simultaneously using a single ChIP-seq protocol. The antibody-DNA adapter conjugates with unique barcodes enable the same assay system to profile various histone modifications, transcription factor bindings, and other protein-DNA interactions without requiring separate specialized assays for each parameter.
2Measurement precision
If multiple assays are performed to screen multiple parameters, then measurement precision is improved, but loss of time increases
Solution Approach 1:
The patent merges multiple sequential ChIP-seq assays into a single parallel assay. By incorporating unique barcodes into antibody-DNA adapter conjugates, the method enables simultaneous profiling of multiple epigenetic marks in one experiment, dramatically reducing the time required compared to performing separate assays for each mark while maintaining comprehensive epigenetic signature detection.
3Measurement precision
If conventional ChIP-seq methods are used, then detection of single modality is achieved, but adaptability decreases
Solution Approach 1:
The patent transforms the conventional single-modality ChIP-seq method into a universal multiplexed platform. By using antibody-DNA adapter conjugates with unique barcodes, the same assay system can adaptively detect various histone modifications, transcription factor bindings, and other protein-DNA interactions, enabling flexible profiling of multiple epigenetic marks without requiring methodological changes for each target.
Solution Approach 2:
The patent changes the key parameter of the assay from single-target detection to multi-target detection by incorporating barcode sequences into the antibody-DNA adapter conjugates. This parameter change allows the system to distinguish and quantify multiple different epigenetic marks simultaneously while maintaining the fundamental ChIP-seq workflow and analysis pipeline.
4Measurement precision
If multiple assays are performed, then comprehensive profiling is achieved, but productivity decreases
Solution Approach 1:
The patent combines multiple separate ChIP-seq assays into a single multiplexed assay, enabling comprehensive epigenetic profiling of multiple histone modifications and protein-DNA interactions simultaneously. This merging approach maintains the depth and precision of individual assays while achieving the comprehensive coverage of multiple assays, thereby improving screening efficiency and productivity.
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 comprehensive profiling of epigenetic signatures and protein-DNA interactions, providing detailed insights into cellular identities and mechanisms, with reduced loss of sequenceable material and cost-effectiveness.
Implementation Method 1
contacting the one or more cell nuclei comprising DNA with one or more first antibodies and one or more first antibody-DNA adapter conjugates, wherein the first antibody is directed against a protein of interest suspected to interact with DNA
Implementation Method 2
allowing the first DNA adapter part of the first antibody-DNA adapter conjugate to ligate to an end of the dephosphorylated DNA fragments
Implementation Method 3
digesting the DNA with a first restriction endonuclease to provide DNA fragments
Implementation Method 4
dephosphorylating the 5'-end of the DNA fragments to provide dephosphorylated DNA fragments
Implementation Method 5
treating the sample obtained after step (b) by degrading protein, preferably by conducting a protein degradation enzyme treatment
Data Source
AI summary
A method for sequencing DNA wherein a sample comprising isolated cell nuclei is contacted with an antibody that forms a covalent conjugate with a first DNA adapter, and wherein the formed antibody-DNA conjugate can bind a protein of interest and ligate to an end of a dephosphorylated DNA fragment, and wherein the sample is then contacted with a second DNA adapter that coheres to the first DNA adapter of the antibody-DNA conjugate to obtain a second DNA adapter—first DNA adapter—DNA fragment product that allows for sequencing of an amplified product.