Nucleic Acid Concatemer Junction Sequencing for Spatial Proximity Mapping
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Solution Overview
Problem
Current methods are inadequate for determining the spatial proximity relationships between nucleic acid sequences in vivo, particularly genomic DNA, due to its enormous size and complex three-dimensional organization, which complicates the study of genome dynamics and disease mechanisms.
Innovation Solution
The method involves fixing nucleic acids in position, fragmenting them, joining fragmented ends to form nucleic acid concatemers with junctions that encode spatial proximity information, and determining the sequence of these junctions to detect spatial relationships between nucleic acid sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If genomic DNA is analyzed to determine spatial proximity relationships, then comprehensive interaction mapping is achieved, but the enormous size and complex three-dimensional organization of genomic DNA makes determination difficult
Solution Approach 1:
The method fragments genomic DNA into smaller pieces before analysis. This segmentation allows manageable handling of the enormous genomic DNA while preserving spatial proximity information through in situ fragmentation, resolving the contradiction between comprehensive mapping and genome complexity
Solution Approach 2:
The method transitions from linear DNA sequence analysis to three-dimensional spatial proximity analysis by ligating fragmented DNA ends based on their physical proximity in the nucleus. This dimensional change enables comprehensive interaction mapping despite the complex three-dimensional organization of genomic DNA
2Productivity
If multiple nucleic acid interactions are simultaneously mapped, then a multidimensional contact map is produced, but the complexity of analyzing numerous interactions increases
Solution Approach 1:
The method performs preliminary ligation of fragmented nucleic acids in situ before any analysis steps. This preliminary action captures all spatial proximity relationships simultaneously, enabling high-throughput multidimensional contact mapping while simplifying subsequent analysis through standardized library preparation
Solution Approach 2:
The method creates concatemer copies that encode spatial proximity information through their sequence composition. These copies can be amplified and analyzed separately, decoupling the complexity of multiple interactions from the analysis process while maintaining high productivity
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 allows for the simultaneous mapping of multiple nucleic acid interactions in a cell, providing a multidimensional contact map that surpasses pairwise contact determination, enabling a deeper understanding of cellular dynamics and potential therapeutic applications.
Implementation Method 1
providing a sample comprising nucleic acids, wherein the nucleic acids are fixed in position relative to one another
Implementation Method 2
joining ends of fragmented nucleic acids to other ends fragmented nucleic acid to create at least one nucleic acid concatemer
Implementation Method 3
using a probe that specifically hybridizes to the at least one junction both 5′ and 3′ of the site of the at least one junction
Data Source
AI summary
Disclosed are methods for detecting spatial proximity relationships between nucleic acid sequences in a cell. The methods include: providing a sample of one or more cells comprising nucleic acids; fragmenting the nucleic acids present in the cells, wherein the fragmented nucleic acids have ends capable of joining to other fragmented nucleic acids; joining ends of fragmented nucleic acids to other ends fragmented nucleic acid to create at least one nucleic acid concatemer having at least one junction between the joined fragmented nucleic acids, and wherein the at least one nucleic acid concatemer encodes the information about the proximity of the DNA sequences in the cell; and determining the sequence at least one junction of the at least one nucleic acid concatemer, thereby detecting spatial proximity relationships between nucleic acid sequences in a cell.