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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

CRISPR

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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

Homologous Recombination

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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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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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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.
The recognition sites for Cre recombinase called LoxP...
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Updated: Sep 17, 2025

A Universal Protocol for Large-scale gRNA Library Production from any DNA Source
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CRISPRware: a software package for contextual gRNA library design.

Eric Malekos1, Christy Montano2, Susan Carpenter3

  • 1Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA. emalekos@ucsc.edu.

BMC Genomics
|July 2, 2025
PubMed
Summary
This summary is machine-generated.

CRISPRware is a new method for designing guide RNA (gRNA) libraries that considers genetic variations for precise gene editing. This tool identifies effective gRNAs across six organisms, aiding CRISPR-Cas9 and CRISPR-Cas12A applications.

Keywords:
CRISPR screenGuide RNANext generation sequencing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • CRISPR-Cas systems offer powerful genome editing capabilities.
  • Designing effective guide RNAs (gRNAs) is crucial for CRISPR technology success.
  • Current methods may not fully account for genetic variations or target diverse genomic regions.

Purpose of the Study:

  • To introduce CRISPRware, an efficient computational method for designing guide RNA libraries.
  • To enable the design of context-specific and allele-specific gRNAs.
  • To create a publicly accessible resource of high-quality gRNAs for Cas9 and Cas12A.

Main Methods:

  • CRISPRware utilizes next-generation sequencing data for gRNA design.
  • The method incorporates genetic variation analysis for allele-specific targeting.
  • It identifies and scores gRNAs against transcribed, translated, and noncoding regions.

Main Results:

  • CRISPRware successfully designed gRNA libraries for six model organisms.
  • The tool identified and scored gRNAs targeting coding sequences for Cas9 and Cas12A.
  • A publicly available resource of these gRNAs was hosted on the UCSC Genome Browser.

Conclusions:

  • CRISPRware provides an efficient and versatile platform for gRNA library generation.
  • The tool's ability to handle genetic variation enhances precision in genome editing.
  • The public resource facilitates broader adoption and application of CRISPR technologies across model organisms.