Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA as a Genetic Template02:05

DNA as a Genetic Template

22.7K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
22.7K
Homologous Recombination02:31

Homologous Recombination

52.0K
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
52.0K
DNA Microarrays02:34

DNA Microarrays

18.4K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
18.4K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.1K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.1K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A uniform tissue-clearing framework and mesoSPIM-ultra enable cm-scale single-neuron tracing.

bioRxiv : the preprint server for biology·2026
Same author

Evolving Roles of Primary Cilia in CNS Development and Neural Circuit Function: From Human Disease to Molecular Underpinnings.

The Journal of neuroscience : the official journal of the Society for Neuroscience·2026
Same author

Hoxc13 and homologs of mammalian hair keratins are required for the cornification of nuptial pads in Xenopus frogs.

Communications biology·2026
Same author

SIX1 branchio-oto-renal syndrome variants have different effects on embryonic craniofacial gene expression and cartilage formation.

Development (Cambridge, England)·2026
Same author

Altair-dvOPM: an open-access platform for large-field three-dimensional tissue imaging.

bioRxiv : the preprint server for biology·2026
Same author

Glomage: A Multimodal Platform for High-Content Morphological and RNA Profiling of Glomeruli in Zebrafish and Mouse Models.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Related Experiment Video

Updated: Sep 11, 2025

Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates
06:10

Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates

Published on: May 9, 2025

433

Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates.

Thomas Naert1,2, Taiyo Yamamoto3,4, Shuting Han5,6,7

  • 1Institute of Anatomy, University of Zurich, Zurich, Switzerland. thomas.naert@ugent.be.

Nature Biotechnology
|August 12, 2025
PubMed
Summary

Precise CRISPR DNA integration is now predictable using deep learning. New repair strategies ensure accurate gene editing and cassette insertion, advancing genetic engineering applications.

More Related Videos

CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy
08:22

CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy

Published on: March 12, 2018

15.0K
Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

362

Related Experiment Videos

Last Updated: Sep 11, 2025

Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates
06:10

Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates

Published on: May 9, 2025

433
CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy
08:22

CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy

Published on: March 12, 2018

15.0K
Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

362

Area of Science:

  • Genetics and Genomics
  • Molecular Biology
  • Bioengineering

Background:

  • CRISPR-based genome editing offers powerful tools but precise DNA integration and editing remain challenging due to limited control over cellular repair mechanisms.
  • Existing methods often result in unpredictable outcomes, including unwanted deletions and insertions, hindering their application in research and therapeutics.

Purpose of the Study:

  • To develop a predictable and controllable method for precise CRISPR-based DNA integration and editing.
  • To improve the efficiency and accuracy of gene insertion and modification using sequence-context-specific repair strategies.

Main Methods:

  • Utilized deep learning models to predict DNA repair outcomes at the genome-cargo interface based on sequence-context rules.
  • Designed and implemented base-pair tandem repeat repair arms that match microhomologies at double-strand breaks.
  • Validated the strategy across diverse cell types and organisms, including HEK293T cells, Xenopus, and mouse brains, for both germline and somatic applications.

Main Results:

  • Demonstrated predictable DNA repair and precise integration of genetic cassettes at 32 loci in HEK293T cells.
  • Achieved germline-transmissible transgene integration and successful endogenous protein tagging in Xenopus and mouse brains.
  • Showcased scarless single-nucleotide and double-nucleotide edits using optimized repair arms and oligonucleotide templates in vitro and in vivo.
  • Developed Pythia, a design tool to facilitate precise genomic integration and editing.

Conclusions:

  • Precise CRISPR-based DNA integration and editing are achievable through predictable, sequence-context-specific repair mechanisms.
  • The developed strategy significantly enhances the accuracy and efficiency of gene editing, reducing unwanted byproducts.
  • This approach holds broad potential for experimental genomics, gene therapy, and synthetic biology applications across various cell types and organisms.