Comparison Between Prime Editing and CRISPR-Cas9

Comparison Between Prime Editing and CRISPR-Cas9

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What is CRISPR-Cas9?

CRISPR-Cas9 is a gene editing technology that has changed the landscape of biological research. It stands for Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-Associated Protein 9. CRISPR-Cas9 uses a two-component system consisting of a guide RNA (gRNA) and a Cas9 protein. The gRNA is designed to complement specific target sequences in the genome to guide the Cas9 protein to the desired location. Once the Cas9 protein reaches the target site, it causes a double-strand break in the DNA helix, which initiates a cellular repair process that can lead to gene modification or insertion.  Explore with our CRISPR Screen Sequencing Data Analysis Service and CRISPR Validation Sequencing Data Analysis Service for more information.

How CRISPR-Cas9 Works?

The mechanism of CRISPR-Cas9 involves a series of steps that ultimately lead to targeted gene editing. First, the gRNA is designed to complement the desired target gene sequence. The Cas9 protein forms a complex with the gRNA and scans the genome to identify matching sequences. Once a match is found, the Cas9 protein binds to the DNA and induces a double-strand break. This break triggers a cellular repair mechanism, which can repair DNA by introducing small insertions or deletions (insertion deletions) or by integrating donor DNA templates for precise editing.

The CRISPR/Cas9 system.Fig. 1. The CRISPR/Cas9 system. (Redman M, et al, 2016)

Advantages of CRISPR-Cas9

CRISPR-Cas9 has several advantages that have led to its widespread adoption in genetic research.

  • The commendable versatility of CRISPR-Cas9 empowers researchers to traverse the entire spectrum of biological organisms, ranging from unicellular bacteria to complex multicellular entities, such as plants, animals, and even the intricately structured human genome. This unprecedented adaptability transcends the traditional boundaries of genetic exploration, enabling scientists to unravel the intricate functioning of genes across diverse species. By discerning the fundamental role these genes play in various biological processes, the comprehensive utilization of CRISPR-Cas9 fuels a profound comprehension of the intricate interconnectedness governing the web of life.
  • Moreover, the sheer expediency and cost-effectiveness bestowed by CRISPR-Cas9 in genome editing endeavors contribute to its unparalleled appeal, transcending conventional genetic methodologies. This revolutionary tool expedites the pace of genetic research and discovery by enabling rapid and precise modifications to the genomic landscape, unshackling scientific communities from the burden of laborious and time-intensive procedures. The ease of use and unwavering efficiency of CRISPR-Cas9 seamlessly integrate into the scientific workflow, thereby amplifying research productivity and accelerating breakthroughs in genetic inquiry.

Disadvantages of CRISPR-Cas9

Despite its extraordinary capabilities, CRISPR-Cas9 does have certain limitations and challenges. One major issue is the off-target effect, in which Cas9 may introduce unintended modifications at sites similar to the target sequence. Although efforts have been made to minimize off-target effects through improved gRNA design and Cas9 variants with higher specificity, this remains an ongoing area of research and optimization. There are also significant ethical dilemmas and regulatory hurdles surrounding the ethical considerations of using CRISPR-Cas9 in germline editing and human embryos.

What is Prime Editing?

Prime Editing is a novel gene editing technology that builds on CRISPR-Cas9 but provides additional features for precise modifications. Prime Editing extends the range of edits that can be made to the genome beyond what can be achieved with CRISPR-Cas9 alone. It combines a modified Cas9 protein with reverse transcriptase and a primary editing guide RNA (pegRNA) to achieve targeted changes in DNA sequences without the need for double-strand breaks.

How Prime Editing Works?

Prime Editing uses a more complex mechanism than CRISPR-Cas9 to provide greater precision in genome editing. The pegRNA consists of a hybrid RNA-DNA molecule containing the desired editing sequence, primer binding sites, and a reverse transcription template. The modified Cas9 protein, called the primary editor, is primed by the pegRNA to the target site. Once the target site is reached, the primary editor performs a two-step process. First, the primary editor cuts a gap in a DNA strand, forming a flap that serves as a template for reverse transcription. Reverse transcriptase then uses the pegRNA template to synthesize a new DNA strand, thereby integrating the precise edit into the genome.

Mechanism of prime editing.Fig. 2. Mechanism of prime editing. (Zhao Z, et al, 2023)

Advantages of Prime Editing

Prime Editing offers several advantages over CRISPR-Cas9, particularly in terms of precision and versatility.

  • One of the primary advantages of Prime Editing lies in its ability to achieve precise alterations in the genome without the reliance on double-strand breaks. This crucial distinction mitigates the inherent risk of off-target effects, a concern that has plagued traditional gene editing methods. The enhanced precision of Prime Editing proves especially valuable when tackling precision editing tasks or rectifying point mutations intricately linked to genetic disorders. By circumventing the risk of erroneous modifications in unintended genomic regions, Prime Editing demonstrates its superiority in enabling accurate and tailored genetic interventions.
  • Moreover, Prime Editing extends the spectrum of edits that can be accomplished, exceeding the base substitutions achievable by CRISPR-Cas9. It empowers researchers and scientists to perform targeted insertions or deletions of specific DNA sequences, further augmenting its applicability and influence in the field of genetic engineering. This groundbreaking feature endows Prime Editing with unparalleled potential for executing intricate and precise modifications within the genome, elevating it to the status of a potent and indispensable tool for genetic research and development.

Disadvantages of Prime Editing

While Prime Editing has brought significant advances, it is not without its limitations. The technology is relatively new and still requires further optimization and validation to improve its efficiency and reduce potential off-target effects. Prime Editing also relies on the delivery of multiple components, including Prime editing proteins, pegRNAs, and repair templates, which may pose challenges for some delivery systems or target cell types. In addition, as with any gene editing technology, the ethical considerations surrounding the use of Prime Editing need to be carefully addressed, particularly in the context of germline editing and human applications.


CRISPR-Cas9 and Prime Editing are two remarkable gene-editing technologies that have revolutionized the field of genetic engineering. While CRISPR-Cas9 has been widely adopted and proven to be highly versatile, Prime Editing offers greater precision and extended capabilities to make targeted modifications in the genome. Both technologies have their advantages and disadvantages, and the choice between them depends on the specific goals of the research or therapeutic application. Continued advances in these technologies will undoubtedly shape the future of genetic research and may open up new avenues for the treatment of genetic diseases.


  1. Redman M, King A, Watson C, King D. What is CRISPR/Cas9? Arch Dis Child Educ Pract Ed. 2016 Aug;101(4):213-5.
  2. Zhao Z, Shang P, Mohanraju P, et al. Prime editing: advances and therapeutic applications[J]. Trends in Biotechnology, 2023.
* For Research Use Only. Not for use in diagnostic procedures.
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