One-Sided Transposition Sequencing for DNA Contiguity Preservation
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Solution Overview
Problem
Next generation sequencing technologies face challenges in maintaining contiguity and haplotype information during genomic DNA fragmentation due to the use of transposomes, which can lead to loss of information.
Innovation Solution
Implementing one-sided transposition methods that nick only one strand of double-stranded target DNA, allowing the DNA to remain intact post-transposition, thereby preserving contiguity and haplotype information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If transposomes are used for genomic fragmentation and adaptor ligation, then library preparation is simplified, but contiguity and haplotype information are lost
Solution Approach 1:
The transposome system is segmented into two distinct components: a first transposome that performs fragmentation and adaptor ligation, and a second transposome that performs information-preserving transposition. This segmentation allows each component to specialize in one function, resolving the contradiction between simplification and information preservation.
Solution Approach 2:
The patent introduces an intermediary approach by using two different transposome systems in sequence. The first transposome acts as an initial processor that simplifies library preparation, while the second transposome acts as an information-preserving intermediary that maintains contiguity and haplotype data through one-sided transposition.
2Adaptability or versatility
If double-stranded DNA is fragmented for sequencing, then DNA becomes amenable to next generation sequencing, but information about individual nucleic acid molecules is lost
Solution Approach 1:
The patent applies local quality by making the transposition process asymmetric: one strand of the DNA is fragmented and processed for sequencing, while the other strand remains intact to preserve contiguity and haplotype information. This local differentiation allows simultaneous achievement of sequencing compatibility and information preservation.
Solution Approach 2:
Instead of fragmenting both strands of DNA as in conventional methods, the patent inverts the approach by fragmenting only one strand while leaving the other strand intact. This inverted strategy allows the intact strand to serve as a template for reconstructing contiguity information after sequencing.
3Loss of information
If one-sided transposition is performed, then contiguity information is preserved, but the transposition process must be carefully controlled to nick only one strand
Solution Approach 1:
The patent employs asymmetry in the transposome design by creating a transposome dimer where one monomer is catalytically active and the other is inactive or less active. This asymmetric configuration naturally biases the transposition reaction to occur on only one strand of the DNA, simplifying the control mechanism while preserving contiguity information.
Solution Approach 2:
The patent changes the catalytic activity parameter of the transposome monomers to achieve one-sided transposition. By adjusting the catalytic activity (making one monomer inactive or less active), the system achieves selective nicking of one DNA strand without requiring complex mechanical or structural modifications to the transposome configuration.
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
The method maintains contiguity and haplotype information by ensuring the double-stranded target DNA remains intact, enabling accurate sequencing and phasing of rare alleles and structural variants.
Implementation Method 1
a transposome complex comprising a transposase and a transposon nucleic acid
Data Source
AI summary
Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.