What is CRISPR?

Developing genome-targeting technologies that perform precisely and efficiently is important for genome editing. Genome-editing technologies such as zinc fingers (ZFs) and transcription activator-like effectors (TALEs) enable specific genome modifications but there is a need for new technologies that are more affordable and easy to engineer.


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A class of precise genome-editing tools that utilize nucleases from prokaryotic adaptive immune systems, clustered regularly interspaced short palindromic repeats (CRISPR), was developed. It has shown great applications and potential in the field of genome engineering.

How does it work?

CRISPR and CRISPR-associated (Cas) genes are part of bacterial and archaeal adaptive immune systems that use RNA-guided nucleases to cleave foreign genetic materials. CRISPR refers to a unique set of short, repeated DNA sequences found in the genomes of bacteria. These repeats are interspaced by short variable sequences, known as spacers, which are processed from invading foreign genetic materials such as viruses and integrated into the CRISPR cluster.

Together they make up the CRISPR RNA array (crRNA). The RNA of these spacer sequences acts as a guide RNA (gRNA) to Cas nucleases and leads the nuclease to bind to foreign genetic material that matches these CRISPR sequences. Moreover, multiple gRNAs can be incorporated into a single CRISPR array and this allows simultaneous genome editing of several different sites, with minimal mutagenic activity.

Apart from the gRNA, the nuclease also recognizes a pro-spacer adjacent motif (PAM) sequence, which is a 2-6 base pair DNA sequence immediately following the DNA targeted by the gRNA. The PAM is specific to each type of Cas nuclease.

For example, Cas9 from Streptococcus pyogenes recognizes a 5’-NGG PAM, and those of Neisseria meningitis recognize 5’-NNNGATT, where N represents any nucleotide, and G, A, and T represent guanine, adenosine, and thymine respectively. If a sequence matches the gRNA and has the corresponding PAM sequence, the Cas nuclease binds to the target sequence and cleaves it. Thus, protecting the bacteria from foreign genetic material.

There are many types of CRISPR-Cas systems. The Type II CRISPR system is one of the best characterized. It consists of the nuclease Cas9, the crRNA array, and an auxiliary trans-activating crRNA that processes the crRNA into separate short RNAs.  In prokaryotes, cas9 is a four-component endonuclease that includes two crRNA.

Applications of the CRISPR system

The cas9 endonuclease has been engineered to be a two-component system that fuses the two crRNA into one single gRNA for easy usage of cas9 to find and cut the DNA sequence that matches the gRNA. The target sequence can be easily manipulated by changing the sequence of the gRNA. This allows the CRISPR-Cas system to be used for genome engineering, mainly for knocking-out (to make a gene no longer functional) and knocking-in (one-for-one substitution of DNA sequence in a genetic locus) genes.

Not only can research engineer bacterial genomes, for example, to make a strain that is resistant to viral attacks, CRISPR can also be used to engineer eukaryotic cells. In terms of tackling diseases, a study has shown that CRISPR-Cas systems can target the mutated gene causing the human disease tyrosinemia modeled in mice, by cutting the mutated gene and facilitating homologous recombination to insert the correct, non-mutated copy of the gene into the genome. This paves the way for developing CRISPR to treat human diseases.

In terms of agriculture, CRISPR is also used for creating genetically-modified (GM) crops, for example, making disease-resistant wheat and rice, and thus, ensuring crops harvested would not be damaged by plant diseases.

Ecosystems can also be engineered with CRISPR. One of the most famous examples is gene drive in Malaria-carrying mosquitos. The idea is to use CRISPR to edit genes to make female mosquitoes that transmit Malaria sterile, thus stopping the transmission of Malaria. However, erasing the existence of an entire species would have consequences and disrupt the ecosystem.

Future of CRISPR

Although CRISPR has great potential in genome editing, ethical and safety cautions remain. It is important to ensure that the technology has no off-target effects and introduce mutations elsewhere in the genome.

There are complex regulations for approving the use of CRISPR technologies to ensure their safety. Nevertheless, CRISPR has great potential in providing solutions to problems in Medicine, Agriculture, and Ecology.


  • Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., ... & Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819-823.
  • Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D.A., and Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712.
  • Yin, H., Xue, W., Chen, S., Bogorad, R. L., Benedetti, E., Grompe, M., Koteliansky, V., Sharp, P. A., Jacks, T., & Anderson, D. G. (2014). Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nature Biotechnology, 32(6), 551–553. https://doi.org/10.1038/nbt.2884
  • Hammond, A., Galizi, R., Kyrou, K., Simoni, A., Siniscalchi, C., Katsanos, D., Gribble, M., Baker, D., Marois, E., Russell, S., Burt, A., Windbichler, N., Crisanti, A., & Nolan, T. (2016). A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nature Biotechnology, 34(1), 78–83. https://doi.org/10.1038/nbt.3439

Further Reading

Last Updated: Dec 7, 2020

Christy Cheung

Written by

Christy Cheung

Christy is passionate about communicating science to a wide range of audiences- from the general public to researchers in various fields. She has a BSc in Biological Sciences and is now an MRes student in Biomedical Research Bacterial Pathogenesis and Infection stream at Imperial College London. She has a great interest in tackling the problem of antimicrobial resistance and in translating pre-clinical research into therapeutic solutions.


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