Protocol for detecting interactions within one or more DNA molecules within a cell

A technology of DNA molecules and DNA sequences, applied in the field of detecting the interaction between one or more elements of DNA molecules in cells, which can solve problems such as slow development speed

Pending Publication Date: 2021-12-28
OXFORD NANOPORE TECH LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Existing techniques that are slow to develop include steps that introduce bias

Method used

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  • Protocol for detecting interactions within one or more DNA molecules within a cell
  • Protocol for detecting interactions within one or more DNA molecules within a cell
  • Protocol for detecting interactions within one or more DNA molecules within a cell

Examples

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Embodiment 1

[0087] This example describes an exemplary laboratory workflow applicable to the present disclosure, a method for determining interactions between intracellular elements. Specifically, methods are used to study interactions between genomic elements that are not adjacent in primary sequence. In addition to simplifying assembly, the disclosed methods, when applied to metagenomic samples, provide a means of associating plasmids with their host genomes. An alternative approach for determining the interactions between one or more elements within a DNA molecule employs restriction enzyme digestion to cleave cross-linked DNA prior to performing proximity ligation. However, restriction digestion is time-consuming, and the choice of restriction enzyme is influenced by the nucleotide composition of the genome in the sample, which is not always known in advance—especially when performing metagenomic studies. The present disclosure provides a method to simultaneously lyse cells and split...

Embodiment 2

[0113] This example describes another exemplary laboratory workflow applicable to the present disclosure, a method for determining interactions between intracellular elements. Specifically, methods are used to study interactions between genomic elements that are not adjacent in primary sequence. In addition to simplifying assembly, the disclosed methods, when applied to metagenomic samples, provide a means of associating plasmids with their host genomes. An alternative approach for determining the interactions between one or more elements within a DNA molecule employs restriction enzyme digestion to cleave cross-linked DNA prior to performing proximity ligation. However, restriction digestion is time-consuming, and the choice of restriction enzyme is influenced by the nucleotide composition of the genome in the sample, which is not always known in advance—especially when performing metagenomic studies. The present disclosure provides a method to simultaneously lyse cells and ...

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Abstract

The invention provides a method for detecting interactions between elements within one or more DNA molecules within a cell, wherein the elements are not adjacent in the primary DNA sequence, the method comprising: a) providing a cell in which elements within one or more DNA molecules that are in close proximity are cross-linked; b) simultaneously lysing the cell and mechanically fragmenting the DNA molecules within the cell; c) proximity ligating the one or more fragmented DNA molecules; d) reversing the crosslinks in the ligated DNA molecules; e) sequencing the ligated DNA molecules; and f) analysing the sequencing data to detect interactions between elements within the one or more DNA molecules within the cell.

Description

technical field [0001] The present invention generally relates to a method for detecting interactions between one or more elements within a DNA molecule in a cell, wherein the elements are not adjacent in the primary DNA sequence. Background technique [0002] What is currently needed are techniques that can provide information that can improve the understanding of the spatial organization of the genome. Existing techniques that develop slowly include steps that introduce bias. These biases prevent the resolution of DNA interactions across genome sequences. Contents of the invention [0003] The present inventors have devised novel methods for detecting and resolving interactions between one or more DNA intramolecular elements within a cell. In particular, these methods enable the detection of interacting elements that are not adjacent in the primary DNA sequence. Interaction information can provide an understanding of the conformational features that underpin the hiera...

Claims

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Application Information

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IPC IPC(8): C12Q1/6806C12Q1/6869
CPCC12Q1/6806C12Q2521/501C12Q2523/101C12Q2523/303C12Q2525/191C12Q2535/122C12Q2565/631C12Q1/6855C12Q1/6876
Inventor 戴晓光M·彭德尔顿
Owner OXFORD NANOPORE TECH LTD
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