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Related Concept Videos

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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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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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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CASPER: An Integrated Software Platform for Rapid Development of CRISPR Tools.

Brian Mendoza1, Tanner Fry2, David Dooley1

  • 1Department of Chemical and Biomolecular Engineering and University of Tennessee, Knoxville, Tennessee, USA.

The CRISPR Journal
|July 14, 2022
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Summary

We developed CRISPR Associated Software for Pathway Engineering and Research (CASPER), a flexible tool for designing guide RNAs (gRNAs) in any organism and with any CRISPR-Cas system. CASPER streamlines CRISPR research for diverse applications, including microbiome analysis.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Existing CRISPR design software often targets limited organisms or lacks support for diverse Cas systems and advanced analyses.
  • There is a need for a versatile platform to facilitate broad CRISPR applications across various species and research areas.

Purpose of the Study:

  • To develop a flexible software platform, CASPER, for comprehensive guide RNA (gRNA) generation and analysis.
  • To support any organism and CRISPR-Cas system, including novel features for multitargeting and microbiome analysis.

Main Methods:

  • Development of a user-friendly software platform integrating traditional gRNA design with advanced analytical functions.
  • Implementation of features for multiple Cas-type gRNA generation and evaluation of spacer redundancy within species or microbiomes.

Main Results:

  • CASPER enables gRNA design and analysis for any organism and CRISPR-Cas system.
  • The software provides unique capabilities for multitargeting and microbiome population analyses.
  • Novel features facilitate strain-, species-, or genus-specific CRISPR diagnostic probe design and microbiome manipulation.

Conclusions:

  • CASPER offers a streamlined computational environment for researchers utilizing CRISPR-Cas systems.
  • The platform enhances the utility of CRISPR technology for diverse biological research and engineering applications.