Pac-Man like DNA cut-and-paste tool allows larger gene edits

The CRISPR-Cas toolbox allows genetic manipulation of cultured cells, plants and animals on the basis of simpler RNA-guided DNA recognition. It has provided breakthrough scientific opportunities to engineer desirable traits, cure genetic diseases and enable point-of-care diagnostics. A recent study by Joseph Bondy-Denomy and colleagues further equips this toolbox to cut larger chunks of DNA from a cell’s genome.

The enormous power of the CRISPR-Cas toolbox was commemorated this year with the Nobel Prize in Chemistry to two scientists Jennifer Doudna and Emmanuelle Charpentier, who first developed it in 2012. CRISPR-Cas systems are a diverse group of RNA-guided nucleases that give prokaryotes the ability to defend against viral invaders. Encountered with a phage, microbes can capture snippets of foreign genetic elements from viral DNA and incorporate it into their own genomic CRISPR array. Transcription of CRISPR arrays creates CRISPR RNAs (crRNAs) that bind to Cas nucleases and provide specificity by base-pairing with target nucleic acids.

Among the diverse naturally evolved CRISPR-Cas systems, gene editing applications have mostly focussed on single subunit Class 2 CRISPR systems (such as Cas9 and Cas12a). The widely used CRISPR-Cas9 ensemble is frequently referred to as molecular scissors which can rapidly and precisely excise a small bit of DNA at the targeted site. However, the leading Cas9 and Cas12a enzymes are limited in their ability to make large deletions.

Joseph Bondy-Denomy and colleagues in the UCSF Department of Microbiology and Immunology developed a new CRISPR tool where instead of Cas9, they used a Class 1 system whose signature enzyme is Cas31. Cas3, a 3′–5′ single-strand DNA helicase-nuclease enzyme can, unlike Cas9 or Cas12a, degrade much longer stretches of DNA quickly and accurately. Here, they repurposed and optimised this Type 1-C CRISPR system from P. aeruginosa (PaeCas3c) for both endogenous and heterologous genome engineering in four microbial species. They found it to be capable of efficient genome-scale deletions currently not achievable using other methodologies. Using only a single crRNA with modified repeat sequences, they isolated deletions with variable sizes, one as large as 424 kb, suggesting that this Cascade-Cas3 machinery is capable of degrading entire phage genomes.

Running along the length of the DNA and chewing it up like a Pac-Man, the CRISPR-Cas3 tool offers boundless possibilities, including facilitating the interrogation and manipulation of large segments of repetitive and non-coding DNA with unknown functions, having a broad impact on genetic research.


  1. 1.

    Csörgő, B. et al. A compact Cascade–Cas3 system for targeted genome engineering. Nature Methods (2020).

Download references

Author information



Corresponding author

Correspondence to Anam Akhtar.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Akhtar, A. Pac-Man like DNA cut-and-paste tool allows larger gene edits. Commun Biol 3, 709 (2020).

Download citation


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing