Nucleic Acid Block Coding for High-Resolution Genome Imaging
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Solution Overview
Problem
Current methods for analyzing genomic structures struggle to efficiently integrate multiple modalities of measurements, such as chromosome structures, nuclear bodies, RNA, and chromatin marks, especially in reconstructing 3D structures from interactions, and require thousands of rounds of probe interactions, limiting resolution and multiplexing capacity.
Innovation Solution
The method involves diffraction limited locus imaging and nucleic acid block coding, where nucleic acids, chromosomes, and RNAs are assigned to blocks, mapped, and coded with unique identification codes, allowing for simultaneous imaging and reducing the time required by an order of magnitude, enabling distinction of loci within the diffraction limit and multiplexing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If sequential DNA fluorescence in situ hybridization (DNA FISH) is used to image many DNA loci in single cells, then the ability to detect chromosome organization is improved, but the time required and complexity of the process increases significantly
Solution Approach 1:
The patent divides the genome into multiple chromosome blocks, each assigned a unique barcode. Instead of imaging all loci sequentially, the method segments the imaging task into parallel block-level operations, dramatically reducing the number of hybridization rounds required while maintaining high-resolution chromosome organization detection.
Solution Approach 2:
The patent introduces barcode sequences as intermediaries that represent entire chromosome blocks. These barcodes serve as mediators between the physical chromosome structures and the detection system, allowing multiple loci to be imaged simultaneously through a single hybridization event rather than requiring sequential imaging of each locus.
2Measurement precision
If thousands of rounds of probe interactions are performed to achieve high-resolution genomic imaging, then the resolution and multiplexing capacity are improved, but the device complexity and operational difficulty increase
Solution Approach 1:
The patent adds a dimensional transformation by assigning unique barcode identifiers to chromosome blocks in sequence space. This allows the system to distinguish between multiple chromosome blocks using temporal sequencing of barcode detection rather than requiring spatial separation of thousands of individual loci, thereby reducing the operational complexity while maintaining high resolution.
Solution Approach 2:
The patent changes the detection parameter from direct locus-by-locus imaging to block-level barcode imaging. By transforming the detection unit from individual loci to chromosome blocks with unique identifiers, the system achieves high multiplexing capacity with fewer hybridization rounds and reduced operational complexity.
3Ease of operation
If the diffraction limit is used for imaging, then the simplicity of the imaging system is maintained, but the resolution for distinguishing closely spaced loci is insufficient
Solution Approach 1:
The patent performs preliminary organization of the genome into barcode-defined chromosome blocks before imaging. This pre-organization allows the diffraction-limited imaging system to resolve block-level structures clearly, while the barcode information provides the additional resolution needed to distinguish closely spaced loci that would otherwise be indistinguishable under the diffraction limit.
Data Source
AI summary
The present disclosure provides methods for analyzing genomic structures by diffraction limited locus imaging and nucleic acid block coding. The methods allow efficient and scalable imaging, which can be applied to multiplexed RNA/DNA fluorescence in situ hybridization (FISH).