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Related Concept Videos

CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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CRISPR01:59

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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...
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CRISPR and crRNAs02:53

CRISPR and crRNAs

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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Homologous Recombination02:31

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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...
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Related Experiment Video

Updated: Aug 3, 2025

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution
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Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects.

Muhammad Naeem1, Omer S Alkhnbashi2,3

  • 1Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.

International Journal of Molecular Sciences
|April 13, 2023
PubMed
Summary

CRISPR-Cas9 gene editing technology offers precise genetic manipulation. This review covers bioinformatics tools aiding guide RNA design, target selection, and validation to minimize off-target effects in genome editing experiments.

Keywords:
CRISPR/Cas9base editorsbioinformaticsdeep learningmachine learningoff-target effectsprime editingsgRNAtools

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • CRISPR-Cas9 is a revolutionary gene editing technology enabling precise genetic manipulation across species.
  • The rapid evolution of CRISPR-Cas technology necessitates advanced bioinformatics tools for experimental efficiency.

Purpose of the Study:

  • To review computational tools for assessing CRISPR-Cas9 off-target effects and quantifying nuclease activity/specificity.
  • To guide researchers in optimizing tools for gene knock-out (KO) and gene knock-in (KI) in model organisms.

Main Methods:

  • Review of existing bioinformatics tools, including web-based platforms.
  • Discussion of experimental validation methods for nuclease activity and specificity.
  • Analysis of tool optimization for gene editing applications.

Main Results:

  • A comprehensive overview of bioinformatics tools for CRISPR-Cas9 experimental design and validation.
  • Identification of strategies to minimize off-target effects and enhance nuclease specificity.
  • Insights into optimizing tools for specific gene editing outcomes like KO and KI.

Conclusions:

  • Bioinformatics tools are crucial for advancing CRISPR-Cas9 precision genome editing.
  • Effective tool selection and optimization are key to overcoming challenges in target selection and predicting off-target effects.
  • Future directions emphasize enhanced precision and broader applications of genome editing technologies.