Planar Biological Sample Analysis via Spatially Preserved Probe Transfer
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Conventional methods for spatial analysis of biological samples face challenges such as optical crowding, spatial crowding, time consumption, and high background noise, which limit resolution and accuracy in detecting and imaging molecular interactions.
Innovation Solution
A method involving contacting oligonucleotides or conjugates with a planar biological sample, performing in situ reactions to produce reporter probes, transferring these probes to a support while preserving spatial relationships, and detecting them on the support to avoid tissue-related background noise and enable high-resolution imaging.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional amplification-based methods (e.g., RCA) are used to detect molecules in tissue, then detection sensitivity is improved, but spatial resolution deteriorates due to spatial crowding of amplification products
Solution Approach 1:
The patent extracts the detection target (DNA molecules) from the tissue context and transfers it to a solid support for imaging. This separation removes the amplification products from the crowded tissue environment, allowing high-sensitivity detection without spatial crowding artifacts. The DNA molecules are captured on a support surface where they can be imaged at single-molecule resolution without the physical constraints of tissue architecture.
Solution Approach 2:
The patent introduces an intermediary solid support surface that mediates between the tissue sample and the imaging system. This support acts as a transfer medium that preserves spatial relationships while providing a clean background for detection. The intermediary surface enables the separation of detection function from the complex tissue matrix, resolving the contradiction between sensitivity and spatial resolution.
2Adaptability or versatility
If multiplexed assays are performed on tissue sections using conventional methods, then molecular interaction detection capability is improved, but analysis time increases to several days due to sequential imaging requirements
Solution Approach 1:
The patent segments the detection process into two independent phases: (1) in situ hybridization and amplification within the tissue, and (2) transfer and imaging on a solid support. This segmentation allows the complex multiplexed assay to be completed in the tissue without time constraints, then transferred for rapid imaging. The separation of detection and imaging functions eliminates the sequential time bottleneck while maintaining multiplexed capability.
Solution Approach 2:
The patent performs preliminary actions (hybridization, amplification, and molecule capture) within the tissue section before transfer. By completing the complex molecular interactions and amplification steps in the tissue environment first, then transferring the results to a support for imaging, the method eliminates the need for repeated tissue manipulation and imaging cycles, dramatically reducing analysis time while preserving multiplexed detection capability.
3Loss of information
If conventional imaging methods are used to image tissue depth with z-stack, then three-dimensional spatial information is improved, but background noise increases and image quality deteriorates
Solution Approach 1:
The patent extracts the DNA molecules from the three-dimensional tissue context and transfers them to a two-dimensional solid support. This extraction eliminates the need for z-stack imaging through tissue, removing the source of background noise while preserving the spatial relationships of molecules in the plane of interest. The transfer process captures molecular positions without the optical sectioning requirements that generate noise in conventional tissue imaging.
Solution Approach 2:
The patent transitions from three-dimensional imaging through tissue (requiring z-stack) to two-dimensional imaging on a solid support. By changing the dimensionality of the detection plane and transferring molecules to a surface, the method eliminates the depth-related background noise while preserving spatial information in the remaining dimensions. This dimensional transformation resolves the contradiction between obtaining spatial information and avoiding background noise.
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 method allows for high-resolution, multiplexed detection of molecular interactions without optical or spatial crowding, reduces analysis time, and enhances signal-to-noise ratio by immobilizing DNA molecules for sequential labeling, enabling detection of up to 10,000 genes or proteins.
Implementation Method 1
contacting an oligonucleotide or a conjugate comprising the same with a planar biological sample under conditions by which the oligonucleotide or conjugate specifically binds to sites in or on the sample
Implementation Method 2
proximally located target proteins or epitopes are bound by the corresponding antibodies
Implementation Method 3
transferring the reporter probe from the sample to a planar support that does not comprise an array of oligonucleotides, in a way that preserves the spatial relationship of the reporter probe in the sample
Implementation Method 4
labeling RNA with various combinations and designs of fluorescent oligonucleotides
Data Source
AI summary
Provided herein, among other things, is method for analyzing a planar biological sample. In some embodiments, the method may comprise: contacting an oligonucleotide or a conjugate comprising the same with a planar biological sample under conditions by which the oligonucleotide or conjugate specifically binds to sites in or on the sample; performing one or more steps to release and/or extend the oligonucleotide in situ, to produce a reporter probe; transferring the reporter probe from the sample to a planar support that does not comprise an array of oligonucleotides, in a way that preserves the spatial relationship of the reporter probe in the sample; and detecting the reporter probe on the support.