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Related Concept Videos

CRISPR and crRNAs02:53

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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.
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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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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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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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Updated: Dec 31, 2025

CRISPR Guide RNA Cloning for Mammalian Systems
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Computational approaches for effective CRISPR guide RNA design and evaluation.

Guanqing Liu1,2, Yong Zhang1,3, Tao Zhang1,2,4

  • 1Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China.

Computational and Structural Biotechnology Journal
|January 1, 2020
PubMed
Summary

This review covers computational tools for designing guide RNAs in CRISPR gene editing. It helps researchers select optimal tools to improve cleavage efficiency and specificity.

Keywords:
CRISPREfficiencyGuide RNA designMachine-learningSpecificity

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Gene Editing Technologies

Background:

  • The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (Cas) system is a key gene editing technology.
  • Effective CRISPR editing relies on suitable Cas proteins and guide RNAs.
  • Low cleavage efficiency and off-target effects are significant challenges in CRISPR applications.

Purpose of the Study:

  • To review computational approaches for predicting guide RNA (gRNA) cleavage efficiency and specificity.
  • To summarize existing tools and their methodologies for gRNA design.
  • To provide guidance for selecting appropriate computational tools for CRISPR research.

Main Methods:

  • Discussion of various computational approaches for scoring guide RNAs.
  • Focus on the features and computational methods utilized by these scoring systems.
  • Analysis of empirical and machine learning-based scoring methods.

Main Results:

  • Identification of diverse computational strategies for gRNA design.
  • Summary of existing tools, highlighting their strengths and weaknesses.
  • Recommendation of user-friendly web-based tools for practical application.

Conclusions:

  • Computational tools are essential for optimizing CRISPR/Cas system performance.
  • Understanding the methodologies behind these tools aids in selecting the best fit for specific research needs.
  • The review offers a valuable resource for researchers aiming to improve gene editing outcomes through effective gRNA design.