Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

CRISPR

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...

Homologous Recombination

Homologous Recombination

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...

You might also read

Related Articles

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

Sort by

Same author

Design of bacterial DNT sensors based on computational models.

Nucleic acids research·2026

Same author

Designing genetically stable multicopy gene constructs with the ChimeraUGEM web server.

NAR genomics and bioinformatics·2025

Same author

Silent mutations in coding regions of Hepatitis C virus affect patterns of HCV RNA structures and attenuate viral replication and pathogenesis.

Genome biology·2025

Same author

AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.

Science advances·2025

Same author

The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3.

Briefings in bioinformatics·2025

Same author

Translon: a single term for translated regions.

Nature methods·2025

Search research articles

Related Experiment Video

Updated: Jun 14, 2025

Electroporation-Based CRISPR-Cas9-Mediated Gene Knockout in THP-1 Cells and Single-Cell Clone Isolation

Electroporation-Based CRISPR-Cas9-Mediated Gene Knockout in THP-1 Cells and Single-Cell Clone Isolation

Published on: February 28, 2025

Codon usage and expression-based features significantly improve prediction of CRISPR efficiency.

Shaked Bergman¹, Tamir Tuller^2,3

¹Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel.

NPJ Systems Biology and Applications

|September 3, 2024

Summary

This summary is machine-generated.

Computational design of CRISPR guide RNAs (gRNAs) is improving. New features incorporating genomic position and gene proximity enhance predictive models, boosting accuracy for CRISPR experiments.

More Related Videos

Using a Fluorescent PCR-capillary Gel Electrophoresis Technique to Genotype CRISPR/Cas9-mediated Knockout Mutants in a High-throughput Format

Using a Fluorescent PCR-capillary Gel Electrophoresis Technique to Genotype CRISPR/Cas9-mediated Knockout Mutants in a High-throughput Format

Published on: April 8, 2017

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins

Published on: October 18, 2022

Related Experiment Videos

Last Updated: Jun 14, 2025

Electroporation-Based CRISPR-Cas9-Mediated Gene Knockout in THP-1 Cells and Single-Cell Clone Isolation

Electroporation-Based CRISPR-Cas9-Mediated Gene Knockout in THP-1 Cells and Single-Cell Clone Isolation

Published on: February 28, 2025

Using a Fluorescent PCR-capillary Gel Electrophoresis Technique to Genotype CRISPR/Cas9-mediated Knockout Mutants in a High-throughput Format

Using a Fluorescent PCR-capillary Gel Electrophoresis Technique to Genotype CRISPR/Cas9-mediated Knockout Mutants in a High-throughput Format

Published on: April 8, 2017

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins

Published on: October 18, 2022

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

CRISPR genome editing is precise but computationally designing guide RNAs (gRNAs) remains challenging.
Current predictive models often lack accuracy, relying solely on target DNA sequence data.

Purpose of the Study:

To develop novel features for improved computational design of gRNAs.
To enhance the predictive power of models for CRISPR experiments by incorporating genomic context.

Main Methods:

Calculated four new features based on gene expression and codon usage bias indices.
Incorporated target site genomic position and proximity to genes into feature sets.
Trained predictive models using these enhanced feature sets on CRISPR datasets from three cell types.

Main Results:

The new features performed comparably to 425 state-of-the-art features, ranking in the top 2-12%.
Adding expression features significantly improved model r-squared by up to 0.04 (39% relative increase).
Achieved average correlations of up to 0.38 on validation sets, with features deemed important by various metrics.

Conclusions:

Genomic position and gene context are valuable additions to sequence-based features for gRNA design.
Incorporating these features will advance the prediction, design, and understanding of CRISPR experiments.