Whip-seq Biomolecular Interaction Mapping
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for mapping genomic organization of modified histones and DNA binding proteins, such as ChIP-seq, face limitations including inefficiency, inability to profile multiple epitopes simultaneously, and averaging signals from populations of cells, which hinder understanding of cellular states and disease mechanisms.
Innovation Solution
The use of 'Whip-seq' technology, which employs single-stranded nucleic acid molecules with two 3' ends (whip molecules) and DNA barcoding to simultaneously map multiple DNA-binding proteins from a single sample, avoiding immunoprecipitation and enabling high-sensitivity protein complex dynamics analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If ChIP-seq methodology is used to map DNA-associated proteins, then genomic organization can be mapped, but the signal is averaged from population of cells and cannot profile multiple epitopes simultaneously
Solution Approach 1:
The invention segments the detection process by using individual cell isolation (FACS) to separate cells, then applies unique molecular barcodes to track specific epitopes independently in each cell. This allows multiple epitopes to be profiled simultaneously without signal averaging, as each cell's data remains distinct and can be analyzed separately.
Solution Approach 2:
The invention introduces molecular barcodes as intermediaries between the epitopes and the detection system. Each antibody is conjugated to a unique barcode sequence, allowing multiple epitopes to be detected simultaneously through sequencing. The barcodes serve as mediators that preserve individual cell information while enabling multiplexed detection of multiple protein targets.
2Productivity
If standard ChIP-seq is used, then DNA-associated proteins can be mapped, but immunoprecipitation efficiency is low resulting in signal reduction
Solution Approach 1:
The invention replaces the mechanical immunoprecipitation process with a sequencing-based detection method. Instead of using antibodies to pull down DNA-protein complexes through physical manipulation, the method uses antibody-barcode conjugates that are sequenced directly. This substitution eliminates the inefficient immunoprecipitation step while maintaining or improving signal strength through direct molecular detection.
Solution Approach 2:
The invention creates molecular copies of the antibody-epitope interactions through barcode sequences. Each antibody binding event is captured and amplified through DNA sequencing, generating multiple copies of the binding information. This copying mechanism increases detection sensitivity and signal strength without requiring efficient immunoprecipitation.
3Measurement precision
If ChIP-seq is performed on population of cells, then genomic organization can be determined, but individual cell protein complex dynamics cannot be resolved
Solution Approach 1:
The invention performs preliminary cell isolation and individual cell sorting (FACS) before the main detection step. By pre-separating individual cells and assigning unique barcodes early in the process, the method enables subsequent high-resolution analysis of protein complex dynamics in each cell without requiring complex post-processing or analysis methods.
Solution Approach 2:
The invention changes the detection parameter from bulk population averaging to single-cell resolution through FACS sorting. By isolating individual cells and using unique molecular barcodes to track epitopes within each cell, the method transforms the measurement from population-level statistics to single-cell precision, enabling resolution of cell-to-cell variability in protein complex dynamics.
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
Whip-seq allows for high-resolution, cost-effective, and efficient mapping of chromatin regulators, enabling the identification of combinatorial signatures in normal and disease states, guiding therapeutic approaches by analyzing protein complexes on the same genomic molecule from a single cell.
Implementation Method 1
combining in reaction solution (a) a single-stranded nucleic acid comprising two 3′ ends, wherein each 3′ end comprises an anchor domain, (b) a barcoded nucleic acid comprising a primer domain, a barcode domain and a nucleotide domain that is complementary to one of the anchor domains of the single-stranded nucleic acid
Implementation Method 2
extension (polymerization) of the single-stranded-nucleic acid through the primer domain of the barcoded nucleic acid, thereby producing a partially-double-stranded molecule
Data Source
AI summary
The present disclosure, in some aspects, provides compositions, systems and methods for proximity-based detection of target biomolecules of interest.