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

Conserved Binding Sites

Conserved Binding Sites

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...

Mutations

Mutations

Mutations

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

Ligand Binding Sites

Ligand Binding Sites

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...

Mutation, Gene Flow, and Genetic Drift

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).

Viral Mutations

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...

You might also read

Related Articles

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

Sort by

Same author

Optimised genome editing for precise DNA insertion and substitution using prime editors in zebrafish.

eLife·2026

Same author

Enhanced γ-globin reactivation and sickle cell correction through a repressor-to-activator motif switch in the <i>HBG1/2</i> promoters.

Molecular therapy. Nucleic acids·2026

Same author

A highly efficient method to differentiate CGRP-expressing peptidergic nociceptors from human induced pluripotent stem cells.

Stem cell reports·2026

Same author

Integrative analysis of left ventricle and epicardial adipose tissue identifies SDHA and OGDH as candidate targets for ischemic heart disease.

iScience·2026

Same author

A human endothelial and adipose stem cell-based co-culture model for venous malformations.

Angiogenesis·2026

Same author

Aiolos and Eos drive distinct human TH17 functional states.

Cellular and molecular life sciences : CMLS·2026

Search research articles

Related Experiment Video

Updated: Feb 7, 2026

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

Published on: February 26, 2019

Decoding non-random mutational signatures at Cas9 targeted sites.

Amir Taheri-Ghahfarokhi¹, Benjamin J M Taylor², Roberto Nitsch^1,3

¹Translational Genomics, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.

Nucleic Acids Research

|July 23, 2018

Summary

A new computational platform, RIMA, analyzes Cas9-induced mutations to reveal insights into DNA repair pathways like c-MMEJ. This tool enhances understanding of genome editing outcomes and offers strategies for targeted integration.

More Related Videos

Preparing and Injecting Embryos of Culex Mosquitoes to Generate Null Mutations using CRISPR/Cas9

Preparing and Injecting Embryos of Culex Mosquitoes to Generate Null Mutations using CRISPR/Cas9

Published on: September 10, 2020

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

Related Experiment Videos

Last Updated: Feb 7, 2026

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

Published on: February 26, 2019

Preparing and Injecting Embryos of Culex Mosquitoes to Generate Null Mutations using CRISPR/Cas9

Preparing and Injecting Embryos of Culex Mosquitoes to Generate Null Mutations using CRISPR/Cas9

Published on: September 10, 2020

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Cas9-targeted mutation patterns offer insights into nuclease activity and DNA repair in mammalian cells.
Existing analytical frameworks lack the depth to fully extract this valuable information.
Understanding these patterns is crucial for advancing genome editing technologies.

Purpose of the Study:

To introduce Rational InDel Meta-Analysis (RIMA), a novel computational platform for comprehensive analysis of Cas9-induced genetic alterations.
To enable quantitative assessment of the classical microhomology-mediated end joining (c-MMEJ) pathway's contribution to mutations.
To investigate the role of DNA polymerase θ in c-MMEJ using RIMA.

Main Methods:

Development and application of the RIMA computational platform.
Analysis of mutation signatures at 15 Cas9 target sites in human A549 wildtype and A549-POLQ knockout cells.
Comparative analysis to elucidate the role of DNA polymerase θ in c-MMEJ.

Main Results:

RIMA successfully quantifies the contribution of c-MMEJ to Cas9-induced mutations.
The study identified specific mutation signatures linked to DNA polymerase θ activity.
Nucleotide sequence context (e.g., Thymine vs. Guanine before PAM) influences InDel occurrence and type.

Conclusions:

RIMA provides a powerful approach for characterizing Cas9 nucleases and predicting genome editing outcomes with enhanced accuracy.
The findings offer insights into the flexibility of Cas9 nuclease cutting (blunt vs. staggered ends).
This work presents a potential strategy for homology-independent targeted genomic integration.