What is the difference between prime editing and CRISPR/Cas9

The difference between Prime Editing and CRISPR/Cas9 lies in their mechanisms of editing DNA, their efficiency, precision, and the types of genetic modifications they can achieve.

Mechanism of Editing

• CRISPR/Cas9: This system relies on creating double-stranded breaks (DSBs) in the DNA at a target site specified by a guide RNA (gRNA). The cell then repairs these breaks using either non-homologous end joining (NHEJ) or homology-directed repair (HDR), processes that can introduce insertions or deletions (indels) or incorporate donor DNA sequences[3][4].
• Prime Editing: Unlike CRISPR/Cas9, prime editing does not rely on creating DSBs. Instead, it uses a fusion protein consisting of a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase enzyme, guided by a prime editing guide RNA (pegRNA). This system can directly write new genetic information into a specified DNA site without the need for DSBs or donor DNA templates, mediating targeted insertions, deletions, and all 12 types of base-to-base conversions[3][4].

Efficiency and Precision

• CRISPR/Cas9: While powerful, CRISPR/Cas9's reliance on DSBs and the cell's repair mechanisms can lead to unintended indels or off-target effects, which are changes in DNA sequences other than the intended target site. These limitations can affect the efficiency and precision of the editing process[4].
• Prime Editing: Prime editing offers more targeting flexibility and greater editing precision. It allows for the introduction of all types of substitutions, insertions, and deletions with fewer unintended byproducts and off-target effects. This is because prime editing does not require a precisely positioned protospacer adjacent motif (PAM) sequence and does not induce DSBs, reducing the risk of unintended genetic modifications[2][3].

Types of Genetic Modifications

• CRISPR/Cas9: Primarily used for creating indels or for inserting specific sequences through HDR, which is efficient in dividing cells but less so in non-dividing cells. It is limited by the requirement of a PAM sequence near the target site and the types of edits that can be achieved through the cell's natural repair processes[3].
• Prime Editing: Capable of making all 12 possible types of nucleotide substitutions (transitions and transversions), as well as targeted insertions and deletions, without the limitations imposed by PAM sequences or the efficiency of HDR. Prime editing can, in principle, correct about 89% of known pathogenic human genetic variants, offering a broader range of genetic modifications than CRISPR/Cas9[3][4].

In summary, while both Prime Editing and CRISPR/Cas9 are groundbreaking genome editing tools, Prime Editing offers a more precise and versatile approach for making a wider range of genetic modifications with fewer off-target effects and indels, overcoming some of the limitations associated with CRISPR/Cas9's reliance on DSBs and the cell's repair mechanisms.

Citations:
[1] https://www.fiosgenomics.com/prime-editing-crispr-cas9/
[2] https://www.statnews.com/2019/11/06/questions-david-liu-crispr-prime-editing-answers/
[3] https://en.wikipedia.org/wiki/Prime_editing
[4] https://www.science.org/content/article/new-prime-genome-editor-could-surpass-crispr
[5] https://crisprmedicinenews.com/news/explainer-what-is-prime-editing-and-what-is-it-used-for/
[6] https://www.cellandgene.com/doc/base-editing-and-prime-editing-how-they-re-changing-gene-therapy-0001
[7] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503568/
[8] https://www.synthego.com/guide/crispr-methods/prime-editing