Spatial Profiling of Nucleic Acid-Protein Interactions via Hybridization Barcoding
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Solution Overview
Problem
Current methods for spatially detecting protein/nucleic acid interactions and monitoring temporal changes in these interactions in biological samples are limited in their ability to provide comprehensive data on the presence, location, and abundance of these interactions.
Innovation Solution
The development of systems and methods that employ nucleic acid-based probes to selectively bind target proteins in a biological sample, followed by spatial analysis using a second set of probes that hybridize with both target nucleic acids and the first probes bound to proteins, providing spatial information through a capture probe with a spatial barcode.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional methods like EMSA are used to detect protein/nucleic acid interactions, then interaction affinity and sequence specificity can be determined, but the technique is laborious, time-consuming, and has limited throughput
Solution Approach 1:
The patent replaces traditional mechanical/chemical detection methods (EMSA, filter binding) with a nucleic acid-based probe system that uses hybridization and spatial barcoding. This substitution enables automated, high-throughput detection while maintaining the ability to measure interaction affinity and specificity through sequence-specific probe binding.
Solution Approach 2:
The invention transforms the detection approach by changing from bulk solution-based methods to spatially-resolved single-cell methods. By implementing spatial barcoding and single-cell RNA sequencing integration, the system simultaneously achieves high precision in interaction detection and high throughput via parallel processing of multiple cells and spatial locations.
2Loss of information
If spatial profiling methods are used to detect analyte locations in tissue, then spatial heterogeneity can be studied, but only a small handful of analytes can be detected in the context of intact tissue
Solution Approach 1:
The patent creates a universal probe system that can detect multiple analyte types simultaneously. The nucleic acid-based probes are designed to detect both protein/nucleic acid interactions and spatial locations through integrated spatial barcoding, enabling multi-analyte detection in intact tissue without sacrificing spatial resolution.
Solution Approach 2:
The invention adds the dimension of spatial barcoding to traditional interaction detection. By encoding spatial location information within the nucleic acid probes themselves, the system enables simultaneous detection of multiple analytes across different spatial locations within intact tissue, transforming 2D tissue sections into 3D spatially-resolved interaction maps.
3Quantity of substance
If single-cell RNA sequencing is performed to obtain analyte data, then comprehensive analyte information can be obtained, but information regarding the position of the single cell in the parent tissue sample is lost
Solution Approach 1:
The patent introduces spatial barcodes as intermediary elements that bridge single-cell analyte detection with tissue architecture preservation. These barcodes are incorporated into the nucleic acid probes and allow reconstruction of cell positions within the parent tissue context, enabling simultaneous acquisition of comprehensive analyte data and spatial location information.
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 enhanced spatial profiling of interactions between nucleic acids and proteins, allowing for the accurate determination of interaction locations and abundances within biological samples, which is crucial for early disease detection and monitoring cellular changes.
Implementation Method 1
employ a first set of nucleic acid-based probes to selectively bind target proteins in a biological sample
Implementation Method 2
spatial analysis within the permeable matrix using a second set of probes designed to hybridize with both a target nucleic acid and with the first probes bound to the target proteins
Data Source
AI summary
Systems and methods for the enhanced spatial analysis of interactions between nucleic acids and proteins in a biological sample have been developed. The methods employ a first set of nucleic acid-based probes to selectively bind target proteins in a biological sample and functionalize the nucleic acids within the sample to enable embedding within a permeable matrix, such as a gel. The methods then implement probe-based spatial analysis within the permeable matrix using a second set of probes designed to hybridize with both a target nucleic acid and with the first probes bound to the target proteins. The resulting hybridized first and second probes are bound by a capture probe including a spatial recognition barcode to provide spatial information for interactions between nucleic acids and target proteins within the sample.