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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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CRISPR/Cas9 Genome Editing01:28

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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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Caspases01:24

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Caspase, a family of cysteine proteases, serve as effectors in apoptosis. The ced3 gene in C.elegans was first identified to be involved in apoptosis. This gene encodes the ced-3 caspase that is similar to the interleukin-1-beta converting enzyme or ICE in mammals. In addition to apoptosis, caspases also function in the inflammatory response. Inflammatory caspases are essential in activating pro-inflammatory cytokines that recruit immune cells and block the replication of pathogens inside...
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The Antiviral System of Bacteria and Archaea: CRISPR01:23

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CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats is a adaptive immune system found in bacteria and archaea that protects against viral infections. This system enables prokaryotic cells to identify, remember, and neutralize foreign genetic elements, primarily bacteriophages, by storing fragments of the invader’s DNA as a genetic memory.The CRISPR immune response begins during an initial infection. Cas (CRISPR-associated) proteins play a central role in this...
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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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Updated: Jul 12, 2025

Substrate Generation for Endonucleases of CRISPR/Cas Systems
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CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.

Benjamin A Adler1,2, Marena I Trinidad1,3, Daniel Bellieny-Rabelo1,2

  • 1Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.

Nucleic Acids Research
|October 27, 2023
PubMed
Summary
This summary is machine-generated.

CasPEDIA is a new database classifying hundreds of Cas enzymes, including Cas9, Cas12, and Cas13 families. This resource aids researchers in understanding and utilizing diverse CRISPR-Cas systems for biotechnological advancements.

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Last Updated: Jul 12, 2025

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Genomics

Background:

  • CRISPR-Cas enzymes provide RNA-guided bacterial immunity and are foundational to genome editing technologies.
  • Class 2 CRISPR-associated enzymes (Cas9, Cas12, Cas13) have broad applications in research, medicine, and agriculture.
  • The vast genetic and biochemical diversity of these enzymes presents challenges for researchers aiming to harness their functions.

Purpose of the Study:

  • To introduce CasPEDIA, a curated encyclopedia of Cas effector proteins.
  • To provide a standardized classification and comprehensive information resource for diverse Cas enzymes.
  • To facilitate the selection and application of suitable Cas enzymes for biotechnological purposes.

Main Methods:

  • Development of CasPEDIA, a web-based database (http://caspedia.org).
  • Curated integration of hundreds of Cas enzymes from Cas9, Cas12, and Cas13 families, plus related IscB and TnpB proteins.
  • Standardized annotation workflow for nuclease activity, target requirements, and guide-RNA constraints.
  • Implementation of a functional classification scheme (CasID) alongside phylogenetic classification.

Main Results:

  • CasPEDIA offers enzymatic classification for hundreds of Cas enzymes across 27 phylogenetic groups.
  • Enzymes are annotated with nuclease activity, target specificity, and guide-RNA design parameters.
  • The CasID system allows searching by enzymatic function and sequence similarity, complementing existing phylogenetic nomenclature.

Conclusions:

  • CasPEDIA serves as a comprehensive data portal for Cas enzyme properties.
  • The database contextualizes enzymatic characteristics, aiding researchers in biotechnological development.
  • CasPEDIA empowers users to leverage the diverse nucleic-acid targeting capabilities of Class 2 CRISPR-Cas enzymes.