Nucleic Acid Structural Analysis via Methyltransferase Barcoding
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for determining genomic sequence information focus on local sequence data, neglecting structural genomic context, making it difficult to access genomic rearrangements, duplications, and other structural sequence information, which are crucial for understanding genetic health and disease states.
Innovation Solution
The method involves processing a double-stranded DNA sample to create sequence-specific labels, allowing for the analysis of nucleic acid biopolymers without breaking them into individual nucleic acids, using techniques like methyltransferase labeling to generate 'barcodes' that indicate relative positions of specific sequences, enabling the preservation of native genomic structures and direct analysis of large intact genomic molecules.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If conventional sequencing methods are used to obtain local sequence information, then sequencing cost and ease of obtaining sequence data are improved, but structural genomic context and structural sequence information are lost
Solution Approach 1:
The method segments the genome into long intact molecules (e.g., BACs, cosmids, or chromosomal segments) that maintain their native structure, rather than fragmenting them into small reads. This allows simultaneous acquisition of local sequence information through sequencing and structural context through physical mapping of these intact molecules.
Solution Approach 2:
The invention adds a spatial dimension by physically mapping sequence information along the length of intact DNA molecules using techniques like FISH or chromosomal walking. This transforms 1D sequence data into 2D spatial information that preserves genomic context and structural relationships.
2Adaptability or versatility
If cytogenetic methods like karyotyping or FISH are used to visualize genomic structural information, then global view of structural information is obtained, but resolution and sensitivity for detecting small sequence motifs or lesions are reduced
Solution Approach 1:
The method segments the genome into large intact molecules that can be individually analyzed, allowing high-resolution detection of small features within the context of the overall genome structure. This enables simultaneous global and local analysis.
Solution Approach 2:
The invention uses physical mapping techniques as intermediaries between cytogenetic methods and molecular sequencing. These techniques (FISH, chromosomal walking) provide a bridge that maintains both the global structural view and the high resolution needed to detect small sequence motifs.
3Productivity
If DNA is fragmented into individual nucleic acids for analysis, then sequencing and analysis can be performed, but native genomic structures and structural information are destroyed
Solution Approach 1:
Instead of fragmenting DNA into small reads that lose structural context, the method segments the genome into large intact molecules (kilobase to megabase scale) that maintain their native structure during analysis. This allows high productivity while preserving structural information.
Solution Approach 2:
The invention changes the size parameter of DNA fragments from nanoscale reads to microscale intact molecules, enabling simultaneous sequencing and structural analysis without fragmentation. This parameter change allows the DNA to maintain its native conformation during processing.
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 rapid and economical determination of nucleic acid structural information, providing detailed genomic and epigenomic insights without fragmenting DNA, thus improving the resolution and accuracy of genomic analysis and reducing sequencing costs.
Implementation Method 1
processing a double-stranded DNA sample to create sequence-specific labels, allowing for the analysis of nucleic acid biopolymers without breaking them into individual nucleic acids, using techniques like methyltransferase labeling to generate 'barcodes' that indicate relative positions of specific sequences
Data Source
AI summary
Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.