Spatial Array Background Reduction Using Diffusion-Restricted Nuclease
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Solution Overview
Problem
Existing methods for determining the location of target analytes in biological samples fail to provide spatial context and are hindered by high background binding, which interferes with accurate signal detection.
Innovation Solution
The use of a diffusion-restricted nuclease to reduce background binding by contacting an array area not covered by the biological sample, followed by permeabilization and sequence determination of spatial barcodes and target nucleic acids to pinpoint their locations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If a biological sample is disposed onto an array to determine target analyte locations, then spatial information can be obtained, but background binding increases and interferes with accurate signal detection
Solution Approach 1:
The patent extracts and removes background nucleic acids from the array surface before sample application. A nuclease is applied to degrade free nucleic acids in the second area (not covered by biological sample), eliminating the source of background binding signals while preserving target analyte detection capability in the first area.
Solution Approach 2:
The patent performs background reduction as a preliminary step before introducing the biological sample. By pre-treating the array with nuclease to remove background nucleic acids, the system establishes optimal detection conditions beforehand, preventing background interference from compromising subsequent measurements.
2Object-generated harmful factors
If the entire array area is treated with nuclease to reduce background, then background binding decreases, but the biological sample in covered areas is also degraded
Solution Approach 1:
The patent applies nuclease treatment selectively to different areas of the array. The first area (covered by biological sample) is protected from nuclease to preserve sample integrity, while the second area (not covered by sample) is treated with nuclease to reduce background binding. This spatially differentiated treatment resolves the contradiction between background reduction and sample preservation.
Solution Approach 2:
The patent divides the array into distinct functional zones: a first area where biological sample is disposed and protected, and a second area where background reduction is performed. This segmentation allows independent optimization of each zone - preserving sample in the first area while eliminating background interference in the second area.
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 significantly improves the signal-to-noise ratio and sequencing yield by reducing background binding, allowing for precise localization of target analytes with enhanced spatial resolution.
Implementation Method 1
contacting the second area of the array with a solution comprising a diffusion-restricted nuclease
Implementation Method 2
diffusion-restricted nuclease
Implementation Method 3
the capture domain binds to the target nucleic acid in the first area
Data Source
AI summary
Provided herein are methods of determining a location of a target analyte in a non-permeabilized biological sample and methods of reducing background binding of an analyte on an array.