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

Mechanical Efficiency of Real Machines01:14

Mechanical Efficiency of Real Machines

1.3K
The mechanical efficiency of a machine is a fundamental concept that describes how effectively a machine can convert input work into output work. According to this concept, the efficiency of a machine is equal to the ratio of the output work to the input work. An ideal machine, meaning a machine that has no energy losses, has an efficiency of one. This implies that the input work and the output work are equal.
However, in reality, no machine can be truly ideal, and all of them experience some...
1.3K
RNA Editing02:23

RNA Editing

9.9K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
9.9K
Nucleotide Excision Repair01:08

Nucleotide Excision Repair

40.8K
Overview
40.8K
Nucleotide Excision Repair01:38

Nucleotide Excision Repair

5.1K
DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
5.1K
Conserved Binding Sites01:49

Conserved Binding Sites

5.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.1K
Ligand Binding Sites02:40

Ligand Binding Sites

15.0K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.0K

You might also read

Related Articles

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

Sort by
Same author

Comparison of single-cell sequencing technologies for allele-specific expression analysis in rabbit spermatids.

Genomics·2026
Same author

Nuc domain electrostatics drive the trans cleavage activity of CRISPR-Cas12a.

Nucleic acids research·2026
Same author

Democratising high performance computing for bioinformatics through serverless cloud computing: A case study on CRISPR-Cas9 guide RNA design with Crackling Cloud.

PLoS computational biology·2025
Same author

Bioinformatic assessment of allergenicity, virulence, and secondary metabolites in Aspergillus species for industrial applications.

Computational biology and chemistry·2025
Same author

Privacy-hardened and hallucination-resistant synthetic data generation with logic-solvers.

Bioinformatics (Oxford, England)·2025
Same author

CRISPR-Cas12a REC2-Nuc interactions drive target-strand cleavage and constrain trans cleavage.

Nucleic acids research·2025

Related Experiment Video

Updated: Jan 28, 2026

CRISPR-Cas9-Mediated Precise Knock-In Edits in Zebrafish Hearts
06:52

CRISPR-Cas9-Mediated Precise Knock-In Edits in Zebrafish Hearts

Published on: September 13, 2022

4.0K

Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning.

Aidan R O'Brien1,2, Laurence O W Wilson1, Gaetan Burgio3

  • 1CSIRO, Sydney, NSW, Australia.

Scientific Reports
|February 28, 2019
PubMed
Summary

We identified key factors influencing gene editing efficiency using machine learning. Our findings significantly improve homology-directed repair (HDR) outcomes and led to the development of a novel tool for designing optimal editing strategies.

More Related Videos

A Machine Learning Approach to Design an Efficient Selective Screening of Mild Cognitive Impairment
12:18

A Machine Learning Approach to Design an Efficient Selective Screening of Mild Cognitive Impairment

Published on: January 11, 2020

7.9K
CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans
09:56

CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans

Published on: November 14, 2018

12.6K

Related Experiment Videos

Last Updated: Jan 28, 2026

CRISPR-Cas9-Mediated Precise Knock-In Edits in Zebrafish Hearts
06:52

CRISPR-Cas9-Mediated Precise Knock-In Edits in Zebrafish Hearts

Published on: September 13, 2022

4.0K
A Machine Learning Approach to Design an Efficient Selective Screening of Mild Cognitive Impairment
12:18

A Machine Learning Approach to Design an Efficient Selective Screening of Mild Cognitive Impairment

Published on: January 11, 2020

7.9K
CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans
09:56

CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans

Published on: November 14, 2018

12.6K

Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • CRISPR-Cas base editing has limitations in nucleotide change types and target site proximity.
  • Homology-directed repair (HDR) offers versatility but suffers from lower efficiency.
  • Optimization factors for HDR have been largely immutable in experimental settings.

Purpose of the Study:

  • To investigate factors governing homology-directed repair (HDR) efficiency using a novel mouse dataset.
  • To identify sequence-specific features of repair templates that influence editing outcomes.
  • To develop a computational tool for optimizing nucleotide editing strategies.

Main Methods:

  • Utilized machine learning on a mouse dataset to analyze variable efficiency-governing factors in HDR.
  • Investigated the role of single-stranded oligodeoxynucleotide (ssODN) sequence composition and regional influence on repair efficiency.
  • Developed a predictive model to enhance HDR efficiency.

Main Results:

  • Discovered that the sequence composition of the single-stranded oligodeoxynucleotide (ssODN) is a critical factor in HDR efficiency.
  • Demonstrated that different regions of the ssODN exert variable influence, correlating with the repair mechanism.
  • Achieved an 83% improvement in HDR efficiency compared to traditional target selection methods.

Conclusions:

  • The sequence composition and regional characteristics of ssODNs are crucial for optimizing HDR efficiency.
  • Developed CUNE (Computational Universal Nucleotide Editor) for designing optimal gene editing strategies.
  • CUNE enables efficient nucleotide editing via traditional base editing or HDR.