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The Antiviral System of Bacteria and Archaea: CRISPR

The Antiviral System of Bacteria and Archaea: CRISPR

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 defense.

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 Short...

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 Short...

CRISPR and crRNAs

CRISPR and crRNAs

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 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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Updated: Jun 3, 2026

Substrate Generation for Endonucleases of CRISPR/Cas Systems

Substrate Generation for Endonucleases of CRISPR/Cas Systems

Published on: September 8, 2012

Structural basis for CRISPR RNA-guided DNA recognition by Cascade.

Matthijs M Jore¹, Magnus Lundgren, Esther van Duijn

¹Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands.

Nature Structural & Molecular Biology

|April 5, 2011

Summary

The CRISPR-Cas system in E. coli uses a Cascade complex to identify foreign DNA. This complex, composed of proteins and RNA, binds target DNA without using energy, enabling continuous surveillance.

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Area of Science:

Molecular Biology
Microbiology
Genetics

Background:

Prokaryotic CRISPR-Cas systems provide adaptive immunity against viruses and plasmids.
The Cascade complex in Escherichia coli is crucial for this immune response.

Purpose of the Study:

To elucidate the composition and structure of the E. coli Cascade complex.
To understand the mechanism by which Cascade recognizes double-stranded DNA (dsDNA) targets.

Main Methods:

Biochemical characterization of the Cascade complex.
Low-resolution structural analysis of Cascade.
Investigation of Cascade-dsDNA interactions.

Main Results:

Cascade is a large ribonucleoprotein complex (405 kDa) with five essential Cas proteins and a 61-nucleotide crRNA.
The crRNA guides Cascade to dsDNA targets via base pairing, forming an R-loop structure.
Cascade binds target DNA sequence-specifically without ATP hydrolysis, indicating energy-independent surveillance.
The complex exhibits an unusual seahorse shape and undergoes conformational changes upon DNA binding.

Conclusions:

Cascade's structure and function are elucidated, revealing an energy-efficient DNA recognition mechanism.
This study provides insights into the molecular basis of CRISPR-Cas immunity in prokaryotes.
The findings suggest a continuous DNA surveillance strategy employed by the CRISPR-Cas system.