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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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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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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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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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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Genome Editing in Mammalian Cell Lines using CRISPR-Cas
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CRISPR-DO for genome-wide CRISPR design and optimization.

Jian Ma1, Johannes Köster2, Qian Qin1

  • 1School of Life Science and Technology, Tongji University, Shanghai 200092, China.

Bioinformatics (Oxford, England)
|July 13, 2016
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Summary

CRISPR-DO is a new web application that helps researchers design better single guide RNAs (sgRNAs) for CRISPR/Cas9 genome editing. It predicts sgRNA efficiency and off-target effects, improving experimental design for various organisms.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • CRISPR/Cas9 technology is popular for genome editing and gene knockout.
  • Effective genome editing relies on well-designed single guide RNAs (sgRNAs).

Purpose of the Study:

  • To develop a web application, CRISPR-DO, for designing and optimizing sgRNA sequences.
  • To support the spCas9 CRISPR system across multiple model organisms (human, mouse, zebrafish, fly, worm).

Main Methods:

  • CRISPR-DO utilizes a computational sequence model to predict sgRNA efficiency.
  • A specificity scoring function assesses potential off-target effects.
  • The tool integrates functional conservation, exon overlap, regulatory sequence, and SNP information.

Main Results:

  • CRISPR-DO provides a user-friendly genome-browser interface.
  • Facilitates selection of optimal target DNA sequences for genome editing experiments.
  • Enables targeting of both coding and non-coding regions.

Conclusions:

  • CRISPR-DO enhances the design process for CRISPR/Cas9 experiments.
  • Improves accuracy and efficiency in genome editing by optimizing sgRNA selection.
  • Supports broad applicability across diverse research fields and model organisms.