Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

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
View PDF0 Cites 0 Cited by
  • 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

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • 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

Experimental program
Comparison scheme
Effect test

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 ...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

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

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
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
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com