Transposase-Mediated Spatial Tagging for High-Resolution Genomic DNA Analysis
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Solution Overview
Problem
Existing methods fail to provide comprehensive spatial analysis of genomic DNA in biological samples, lacking information on the position of single cells within tissues and failing to account for chromatin structure differences between cells.
Innovation Solution
A method involving transposase-mediated transposon insertion into genomic DNA, followed by fragmentation and interaction with capture probes on an array, allowing spatial analysis by correlating probe locations with sample positions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If transposase-mediated transposon insertion is used to analyze genomic DNA, then spatial resolution and measurement precision are improved, but device complexity and manufacturing complexity increase
Solution Approach 1:
The method segments the genomic DNA analysis process into distinct spatially-resolved steps: (1) transposase-mediated insertion of transposons with barcodes at specific genomic loci, (2) fragmentation of DNA, (3) capture of fragments on spatially-addressed arrays, and (4) sequencing. This segmentation enables high spatial resolution by maintaining the connection between physical location and genomic identity throughout the workflow.
Solution Approach 2:
The patent uses transposons as intermediary molecules that serve dual functions: (1) they insert into specific genomic locations to capture spatial information, and (2) they carry barcodes that identify the insertion site. This intermediary approach allows indirect capture of spatial information without requiring direct imaging or manipulation of chromatin structure.
2Loss of information
If comprehensive spatial analysis of genomic DNA is performed, then information completeness is improved, but loss of time and processing duration increase
Solution Approach 1:
The method performs preliminary actions by first inserting transposons with embedded barcodes into genomic DNA at specific locations before any fragmentation or analysis occurs. This preliminary tagging of spatial information allows subsequent steps to proceed in parallel without losing spatial context, reducing overall processing time while maintaining information completeness.
Solution Approach 2:
The patent merges multiple functions into the transposon insertion step: (1) fragmentation of chromatin, (2) tagging of spatial location via barcode insertion, and (3) preparation of DNA for capture. This consolidation of functions reduces the number of separate processing steps required, thereby reducing time loss while achieving comprehensive spatial analysis.
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 high-resolution spatial analysis of genomic DNA, retaining native spatial context and providing insights into transcriptionally active regions and cell function.
Implementation Method 1
providing a transposon sequence and a transposase enzyme to the biological sample under conditions wherein the transposon sequence is inserted into the genomic DNA; allowing the transposase enzyme to excise the inserted transposon sequence from the genomic DNA thus generating fragmented genomic DNA
Implementation Method 2
contacting the biological sample comprising the fragmented genomic DNA with an array under conditions such that a capture probe interacts with the fragmented genomic DNA
Data Source
AI summary
The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.