3D Nucleic Acid Matrix Imaging for Spatial Sequence Reconstruction
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Solution Overview
Problem
Existing optical sequencing methods primarily operate in two-dimensional planes, limiting the reconstruction of nucleic acid sequences and failing to maintain spatial relationships in three dimensions, which is crucial for understanding the function of gene products like RNA and proteins.
Innovation Solution
A method and apparatus for volumetric imaging of nucleic acids within a three-dimensional matrix, utilizing various imaging techniques such as structured illumination, two-photon microscopy, and confocal microscopy to reconstruct three-dimensional positional information of nucleic acid sequences, preserving their spatial relationships and enabling high-throughput sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If two-dimensional solid substrate or microwells are used to immobilize sequencing templates, then spatial invariability for optical detection is maintained, but three-dimensional spatial relationships are lost
Solution Approach 1:
The patent transitions from two-dimensional substrate-based sequencing to three-dimensional matrix-based sequencing. Nucleic acid templates are immobilized within a three-dimensional matrix structure, allowing optical detection to capture spatial information in all three dimensions (x, y, z) rather than being constrained to a single plane. This dimensional expansion preserves the native three-dimensional spatial relationships of nucleic acid templates while enabling volumetric imaging and reconstruction.
2Measurement precision
If optical sectioning methods are used for volumetric imaging, then three-dimensional acquisition of images is achieved, but system complexity increases
Solution Approach 1:
The patent employs an optical sectioning intermediary layer that captures light signals from different focal planes within the three-dimensional matrix. This intermediary optical sectioning mechanism enables volumetric imaging by systematically acquiring images at multiple depths, which are then reconstructed into a complete three-dimensional representation of the nucleic acid templates and their spatial relationships.
3Loss of information
If three-dimensional matrix is used for nucleic acid immobilization, then spatial relationships are preserved, but detection and reconstruction difficulty increases
Solution Approach 1:
The patent segments the three-dimensional imaging space into multiple discrete focal planes or optical sections. By systematically acquiring images at different depths and systematically reconstructing these segmented sections, the complex three-dimensional detection problem is broken down into manageable two-dimensional image acquisition steps, followed by computational reconstruction to assemble the complete volumetric 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
Enables the detection and reconstruction of nucleic acid sequences in three dimensions, maintaining spatial relationships and facilitating high-throughput sequencing of biological specimens, providing detailed positional information of nucleic acids and other molecules within cells and tissues.
Implementation Method 1
Volumetric imaging detects fluorescence- or optically-encoded signals in three dimensions
Implementation Method 2
Exemplary volumetric detection methods include both methods for volumetric imaging of optical sections that utilize optical sectioning
Data Source
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AI summary
Methods of volumetric imaging of a three-dimensional matrix of nucleic acids within a cell is provided. An automated apparatus for sequencing and volumetric imaging of a three-dimensional matrix of nucleic acids is provided.