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Prime editing

Prime editing is a versatile genome editing technology that enables the precise installation of small insertions, deletions, and all types of point mutations directly into a target DNA sequence using a single guide RNA, without inducing double-strand breaks or requiring exogenous donor DNA templates.^[1] Developed by Andrew V. Anzalone, Jonathan S. Gootenberg, Omar O. Abudayyeh, and David R. Liu at the Broad Institute of MIT and Harvard, it combines a nickase variant of the Cas9 protein (H840A Cas9) fused to an engineered reverse transcriptase enzyme with a prime editing guide RNA (pegRNA) that both specifies the target site and provides the template for the desired edit.^[1] The process involves nicking the target DNA, reverse-transcribing the edit from the pegRNA into a new DNA flap, and leveraging cellular repair mechanisms to incorporate the change, achieving efficiencies comparable to or higher than homology-directed repair in human cells while minimizing unwanted byproducts like insertions or deletions.^[1] Since its introduction in 2019, prime editing has demonstrated broad applicability across diverse cell types, including human cell lines, primary cells, and non-dividing neurons, where it has successfully corrected pathogenic mutations associated with diseases such as sickle cell disease (via a T-to-A transversion in the HBB gene) and Tay-Sachs disease (via a 4-bp deletion in HEXA).^[1] It offers advantages over traditional CRISPR-Cas9 nucleases by avoiding double-strand breaks that can lead to genomic instability or p53-mediated cell cycle arrest, and over base editing by accommodating a wider range of modifications, potentially addressing up to 89% of known human genetic variants linked to disease.^[1] Early versions like PE1 (original system) achieved up to 20-50% editing efficiency for certain transitions, but subsequent optimizations have significantly enhanced performance.^[1] Key improvements include the PE2 system, which incorporates an optimized Moloney murine leukemia virus (MMLV) reverse transcriptase to boost efficiency by 1.6- to 5.1-fold; PE3, which adds a second single-guide RNA (sgRNA) to nick the non-edited strand for up to 4.2-fold gains; and PEmax, featuring nuclear localization signal enhancements and codon optimization for further 2- to 3-fold increases.^[2] Additional variants such as ePEs (with engineered pegRNAs for 3' extension protection) and PE4/PE5 (using MLH1 knockdown to inhibit mismatch repair and improve precision by 7-fold) have expanded capabilities to include larger edits, such as insertions up to 1 kb and deletions exceeding 10 kb.^[2] TwinPE and related systems enable multiplexed editing and sequence replacements up to 113 bp with efficiencies approaching 90%, while applications have extended to disease modeling, functional genomics screens, and in vivo corrections in mouse models for conditions like Duchenne muscular dystrophy (28% efficiency) and Huntington's disease (CAG repeat disruption).^[3] As of 2025, prime editing has entered early clinical trials, including the first human application for chronic granulomatous disease, which showed promising safety and efficacy data in mid-2025.^[4] It has demonstrated therapeutic potential in correcting mutations for genetic disorders including phenylketonuria, β-thalassemia, inherited retinal dystrophies, and recessive dystrophic epidermolysis bullosa, where up to 97.5% of mutations are editable in principle.^[3] Challenges persist, including delivery limitations for large payloads, potential off-target effects (though generally lower than Cas9), and activation of cellular stress responses like TP73 or MT2A, but ongoing efforts focus on enzyme optimization, PAM relaxation for broader targeting, and integration with recombinases for gene-sized insertions (>5 kb).^[3] These advancements position prime editing as a promising tool for precision medicine, complementing base editing and other CRISPR technologies in the quest for safer, more flexible genome manipulation.^[2]

Principles of operation

Core components

The prime editor protein is a fusion construct consisting of a catalytically impaired Cas9 nickase (nCas9), specifically the H840A mutant that eliminates endonuclease activity on the target strand while preserving RNA-guided DNA binding and nicking on the non-target strand, linked via a flexible peptide linker to the reverse transcriptase (RT) domain from Moloney murine leukemia virus (M-MLV RT).^[5] This architecture positions the nCas9 domain at the N-terminus for target recognition and the RT domain at the C-terminus for subsequent nucleic acid synthesis, with the H840A mutation being critical to prevent double-strand breaks (DSBs).^[5] In the original prime editing system (PE1), the M-MLV RT is unmodified, but an enhanced variant (PE2) incorporates five key mutations in the RT domain—D200N, L603W, T306K, W313F, and T330P—to improve reverse transcription efficiency and overall editing precision without altering the core fusion structure.^[5] The prime editing guide RNA (pegRNA) is a chimeric single-guide RNA that extends the standard CRISPR-Cas9 single-guide RNA (sgRNA) by incorporating a 3' extension sequence, enabling it to serve dual roles in targeting and templating the edit.^[5] It comprises three main elements: a spacer sequence (typically 20 nucleotides) complementary to the target DNA for site-specific binding, a scaffold domain that recruits and stabilizes the Cas9 component, and the 3' extension functioning as the reverse transcription template (RTT) that encodes the desired genetic modification, such as point mutations, insertions, or deletions up to 44 nucleotides in length.^[5] Within the 3' extension, the primer binding site (PBS) is a short sequence (typically 13-14 nucleotides) adjacent to the spacer that hybridizes to the nicked DNA, while the RTT provides the template for RT-mediated synthesis; optimal PBS lengths are adjusted based on GC content (ideally 40-60%) to balance stability and efficiency.^[5] The nCas9 component within the prime editor binds to the target DNA in a sequence-specific manner guided by the pegRNA spacer and introduces a single-strand nick on the non-target strand approximately 3-4 nucleotides upstream of the protospacer adjacent motif (PAM), thereby exposing a 3' hydroxyl group on the nicked strand without generating DSBs.^[5] This nicking function relies on the preserved RuvC nuclease domain activity in the H840A mutant, ensuring localized access for downstream components while minimizing genomic instability associated with DSBs in traditional CRISPR-Cas9 editing.^[5]

Editing mechanism

Prime editing operates through a search-and-replace mechanism that enables precise genomic modifications without requiring double-strand breaks (DSBs) or exogenous donor DNA, allowing for all 12 possible base-to-base conversions as well as insertions and deletions (indels) of varying lengths.^[1] The process begins with the prime editing guide RNA (pegRNA), which guides a fusion protein consisting of a nickase Cas9 (nCas9, typically SpCas9 H840A) and a reverse transcriptase (RT, often from Moloney murine leukemia virus, MMLV) to the target DNA site. The spacer sequence of the pegRNA hybridizes with the target DNA, leading nCas9 to form an RNA-DNA hybrid R-loop structure that exposes the non-target strand.^[1]^[6] In the second step, the nCas9 nickase introduces a single-strand nick on the non-target strand, typically 3–4 nucleotides upstream of the protospacer adjacent motif (PAM) sequence, generating a 3' hydroxyl end on the nicked DNA. This nick is crucial for initiating the editing process by providing a primer for subsequent reverse transcription. The exposed 3' end then anneals to the primer binding site (PBS) of the pegRNA, a short complementary sequence (typically 8–15 nucleotides long) adjacent to the reverse transcription template (RTT) in the pegRNA.^[1]^[6] The third step involves reverse transcription, where the RT domain extends the nicked 3' DNA end using the pegRNA's RTT (typically 10–20 nucleotides for small edits, extendable to longer sequences) as a template, synthesizing a new DNA flap that incorporates the desired edit. This flap replaces the original sequence in a targeted manner, with the length of the synthesized flap depending on the RTT design; in the original system, flaps up to approximately 44 nucleotides were demonstrated, though advanced configurations have enabled synthesis of over 100 nucleotides. Efficiency of this step is influenced by PBS and RTT lengths, as longer sequences can enhance stability but may reduce processivity if mismatched.^[1]^[6] Finally, cellular resolution integrates the edited flap into the genome. The displaced 5' flap is cleaved by endogenous flap endonuclease 1 (FEN1), and the edited 3' flap is ligated to the upstream DNA by DNA ligase 1, forming a nicked heteroduplex. Subsequent mismatch repair (MMR) or replication favors retention of the edited strand over the original, completing the installation of the modification. In the original prime editing system, this process achieved editing efficiencies of 20–50% for small changes, such as single-base substitutions or short indels, in human cell lines like HEK293T, varying by target site and pegRNA optimization.^[1]^[6]

Evolution of prime editing systems

Original prime editors

The original prime editing system, designated PE1, consisted of a fusion between a Cas9 H840A nickase (nCas9) and the wild-type reverse transcriptase (RT) from Moloney murine leukemia virus (M-MLV RT), connected by a flexible linker. This configuration enabled basic search-and-replace editing using a prime editing guide RNA (pegRNA), but exhibited low efficiency, achieving approximately 1% correction for certain transition mutations in human cell lines such as HEK293T. A key limitation of PE1 was the susceptibility of pegRNAs to cellular degradation, particularly of the 3' reverse transcription template extension, which reduced the availability of functional guides and contributed to inconsistent performance.^[1] To address these shortcomings, PE2 was developed in 2019 by engineering the RT domain with a series of mutations, including D200N to facilitate template switching by reducing RNase H activity, along with L603W, T330P, T306K, and W313F to enhance thermostability and processivity. These modifications improved prime editing efficiency by 5- to 20-fold compared to PE1 across various edits, including transitions, transversions, insertions, and deletions, with reported rates reaching up to 20% for some substitutions in HEK293T cells. The optimizations in PE2, derived from directed evolution and structural insights, allowed for more reliable reverse transcription of the pegRNA template while maintaining the core nCas9-RT architecture.^[1] PE3 further advanced the system by incorporating an additional single-guide RNA (sgRNA) to nick the non-edited DNA strand, typically 1-100 nucleotides away from the edit site, thereby biasing cellular repair pathways toward the incorporation of the edited strand and reducing competition from error-prone mechanisms. This strategy boosted editing efficiency to approximately 50% for targeted substitutions and small indels in human cells, representing a 1.5- to 4-fold increase over PE2, though it also elevated indel byproduct rates to an average of 6.8%. Data from the Liu laboratory demonstrated these gains in diverse genomic contexts, highlighting PE3's utility for higher-throughput applications despite the trade-off in specificity.^[1] Protein engineering efforts led to the development of PEmax, an optimized version of PE2 featuring a human codon-optimized reverse transcriptase, an extended linker with SV40 and c-Myc nuclear localization signals (NLS), and Cas9 mutations (R221K and N394K) to enhance nuclear localization and stability. PEmax achieved 2.5- to 2.8-fold higher editing efficiencies compared to PE2 across seven substitution edits in HeLa and HEK293T cells.^[7] Subsequent refinements led to PE4, which involves co-expression of a dominant-negative MLH1 protein (MLH1dn) with the PE2 architecture to transiently inhibit the mismatch repair (MMR) pathway, preventing degradation of the edited strand and thereby increasing precision for substitution edits. This modification enhanced overall editing efficiency by an average of 7.7-fold across 191 diverse edits at 20 genomic loci in seven mammalian cell types compared to earlier systems, while reducing indel byproducts by 2.4-fold. PE4's approach was particularly effective for prime editing outcomes sensitive to MMR, such as certain point mutations, without permanently disrupting cellular repair functions.^[7] Finally, PE5 combines the nicking strategy of PE3 with MLH1dn inhibition through co-expression, using a pegRNA and an sgRNA to further optimize indel efficiency. This configuration achieved up to 2-fold improvements in insertion and deletion rates over PE4, with average enhancements of 7.7-fold in substitution efficiency and reduced byproducts, making it suitable for a broader range of structural edits in mammalian cells. Evaluations from the Liu laboratory confirmed PE5's superior performance in minimizing unwanted indels while preserving high fidelity for intended changes.^[7]

Advanced variants

Since the initial development of prime editing, researchers have introduced several advanced variants to address limitations in efficiency, editing scope, and stability, particularly for challenging genomic modifications. These post-2020 innovations build on the core prime editing framework by enhancing pegRNA functionality, enabling larger or more complex edits, and incorporating double-strand breaks where precision can be traded for higher throughput.^[8]^[9]^[10]^[11] Engineered pegRNAs (epegRNAs), introduced in 2021, incorporate structured RNA motifs such as MS2 hairpins at the 3' terminus to recruit stabilizing proteins like MCP, thereby extending pegRNA half-life and protecting the reverse transcriptase template from degradation. This modification boosts prime editing efficiency by 3- to 4-fold in cell lines including HeLa, U2OS, and K562, as well as in primary human fibroblasts, without increasing off-target editing. In some optimized contexts, epegRNAs have enabled editing efficiencies approaching 90% for specific substitutions in HEK293T cells when combined with enhanced prime editors.^[8] Twin prime editing (twinPE), developed in 2021, employs dual pegRNAs to direct simultaneous edits on opposite DNA strands, facilitating large-scale modifications such as insertions exceeding 100 nucleotides, deletions, replacements, and inversions without inducing double-strand breaks. This approach leverages two prime editor complexes to generate complementary DNA flaps that are resolved by cellular repair machinery, achieving efficiencies up to 90% for certain sequence replacements with minimal indel byproducts. TwinPE expands the versatility of prime editing for applications requiring bidirectional or extended edits.^[9] Nuclease-based prime editing (PEn), advanced in 2023, fuses the full Cas9 nuclease—rather than a nickase—to the reverse transcriptase, intentionally creating double-strand breaks at target sites to enhance editing in regions with suboptimal PAM sequences or low nickase efficiency. While this trades some precision for higher throughput by harnessing homology-directed repair alongside prime editing, upgraded versions mitigate unwanted indels and achieve versatile outcomes like precise insertions and substitutions at rates surpassing standard prime editors in primary cells. PEn is particularly useful for hard-to-edit genomic loci.^[10] The prime editing for inversions (PIE) system, published in November 2025, utilizes paired pegRNAs to enable precise chromosomal rearrangements, including inversions of segments from kilobases to entire chromosome arms, without detectable off-target effects. PIE variants, such as PIEv3, direct two prime editing events to create and resolve inversion junctions accurately, outperforming nuclease-dependent methods in efficiency and fidelity for structural variant modeling in mammalian cells. This tool holds promise for studying and correcting large-scale genomic aberrations.^[11]

Historical development

Initial discovery

Prime editing was invented in the laboratory of David R. Liu at the Broad Institute of MIT and Harvard University, building on the limitations of CRISPR-Cas9 systems, which often produce unintended insertions or deletions due to double-strand breaks, and extending principles from base editing developed in the same lab.^[1] The method was first described in a seminal paper published on October 21, 2019, in Nature, titled "Search-and-replace genome editing without double-strand breaks or donor DNA," authored by Andrew V. Anzalone and colleagues.^[1] This work introduced prime editing as a versatile CRISPR-based approach that uses a prime editing guide RNA (pegRNA) to specify precise genomic changes, including all 12 types of point mutations, small insertions, and deletions, without requiring external donor DNA or creating double-strand breaks.^[1] The pegRNA design incorporates a spacer sequence for targeting, a reverse transcriptase template encoding the desired edit, and a primer-binding site to initiate the editing process, establishing foundational principles for guide RNA engineering in this system.^[1] In initial experiments, the researchers demonstrated prime editing's efficacy by installing or correcting over 175 different edits across four human cell types (HEK293T, K562, HT29, and HeLa), achieving efficiencies of up to 20–50% for point mutations in HEK293T cells—rates comparable to or higher than homology-directed repair while producing far fewer unintended byproducts than standard CRISPR-Cas9 editing, which often yields indels at rates exceeding 50%.^[1] Notably, 89 of these edits addressed clinically relevant mutations previously difficult to correct, such as the sickle cell disease-associated transversion in the HBB gene (converting A to T at codon 6) and a three-base-pair deletion in the HEXA gene linked to Tay–Sachs disease, with correction efficiencies reaching up to 21% and 53%, respectively, in cell models.^[1] These proof-of-concept results highlighted prime editing's potential for precise, "search-and-replace" genome modification.^[1]

Key milestones

Following the initial development of prime editing in 2019, significant optimizations emerged in 2020 and 2021 to enhance editing efficiency and enable the first in vivo applications. The PE2 system incorporated an engineered reverse transcriptase from Moloney murine leukemia virus, improving the fidelity and efficiency of insertions and transversions compared to the original PE1. Further refinement led to PE3, which added a second single-guide RNA to nick the non-edited strand, boosting overall editing rates up to 5.1-fold in human cells while minimizing insertions and deletions.^[7] In 2021, these systems demonstrated their first in vivo efficacy in mice, achieving precise corrections in the liver for metabolic diseases like hereditary tyrosinemia, with editing efficiencies reaching 11% without off-target effects. In 2022, advancements focused on guide RNA innovations to expand editing scope and precision. The introduction of engineered prime editing guide RNAs (epegRNAs) incorporated motifs that extended RNA half-life, increasing editing efficiency 3- to 4-fold across various cell types without altering specificity.^[8] Concurrently, twin prime editing (twinPE) utilized paired pegRNAs to enable larger-scale modifications, including insertions, deletions, and inversions of up to 10 kb in human cells, with efficiencies up to 23% for replacements exceeding 500 bp. By 2023, prime editing saw broader adoption and specialized variants for diverse applications. Over 100 independent laboratories worldwide had integrated prime editing into their research workflows, reflecting its versatility for precise genome manipulation.^[12] Tools like pegIT, a web-based platform for automated pegRNA design, were released to streamline experiment planning, supporting edits in multiple organisms with specificity checks.^[13] The nuclease-based prime editor (PEn) variant, using full Cas9 nuclease instead of nickase, achieved higher knock-in efficiencies (up to 40%) for small insertions while reducing unintended edits, though it required careful optimization to manage double-strand breaks.^[10] In agriculture, prime editing enabled crop engineering, such as precise allele swaps in rice and wheat for disease resistance, with stable heritable edits in up to 20% of progeny.^[14] In 2024, efforts emphasized multiplexing and preclinical validation. Paired pegRNA systems facilitated simultaneous edits at multiple loci in various models.^[15] Prime Medicine reported preclinical data demonstrating in vivo prime editing in mouse livers, correcting mutations in genes like ATP7B for Wilson's disease with over 20% hepatocyte editing and restored protein function.^[16]

Clinical translation

The clinical translation of prime editing technologies has advanced into human trials as of 2025, with Prime Medicine leading the effort through its PM359 program, the first therapy utilizing prime editing to address chronic granulomatous disease (CGD). PM359 employs an ex vivo approach, correcting mutations in the NCF1 gene within patient-derived CD34+ hematopoietic stem cells to restore neutrophil function.^[17] The U.S. Food and Drug Administration (FDA) cleared the Investigational New Drug (IND) application for PM359 in April 2024, enabling the initiation of a Phase 1/2 open-label, single-arm, multicenter trial evaluating safety and efficacy via autologous transplantation of edited cells.^[18] Initial data from the first patient dosed in the trial, reported in May 2025, demonstrated a favorable safety profile with no serious adverse events observed and evidence of rapid immune restoration, including 58% dihydrorhodamine (DHR) positivity by Day 15 and 66% by Day 30, reflecting efficient editing in hematopoietic cells and functional correction of the p47phox-deficient neutrophils characteristic of autosomal recessive CGD.^[19] In conjunction with this data, Prime Medicine announced a strategic restructuring and is exploring partnerships for further development of PM359, while the trial continues with patient enrollment as of November 2025.^[20]^[21] This trial incorporates advanced prime editing variants, including engineered prime editing guide RNAs (epegRNAs), to optimize specificity and editing outcomes.^[22] Prime editing's broad potential underpins its clinical promise, with the original system capable of addressing approximately 89% of known pathogenic genetic variants associated with human diseases, far exceeding the scope of earlier CRISPR-based tools limited by double-strand breaks. However, challenges persist in the sensitive detection of off-target edits, necessitating refined assays to confirm the technology's low indel byproducts and ensure long-term safety in therapeutic contexts.^[23] Beyond PM359, the pipeline for prime editing in blood disorders continues to evolve, with 2025 updates highlighting ex vivo strategies for conditions like sickle cell disease in early exploration by various biotechs.^[24]

Advantages and limitations

Advantages

Prime editing offers exceptional versatility in genome modification, enabling all 12 possible types of single-nucleotide substitutions, as well as small and large insertions and deletions of up to 44 base pairs, without requiring double-strand breaks (DSBs) or exogenous donor DNA templates.^[1] This capability surpasses base editing, which is restricted to transition mutations (C-to-T and A-to-G), and homology-directed repair (HDR), which demands donor templates and achieves low efficiencies typically below 10% in mammalian cells.^[1]^[25] In principle, prime editing can address approximately 89% of known pathogenic genetic variants associated with human diseases, providing a broad therapeutic scope for conditions like sickle cell disease and cystic fibrosis.^[1] The technology demonstrates high precision, with off-target editing rates averaging ≤0.6% at predicted sites, compared to 32% for conventional CRISPR-Cas9 nucleases under similar conditions.^[26] This reduced off-target activity stems from the requirement for three independent hybridization events in the editing process, enhancing specificity over the single-guide RNA binding in Cas9 systems, where off-target effects can reach 20-50% in some assays.^[26] Additionally, prime editing produces minimal unintended insertions or deletions (<1% byproduct indels), in contrast to Cas9 editing, which often generates 10-20% indels at target sites due to non-homologous end joining repair.^[1] By avoiding DSBs entirely, prime editing circumvents the genotoxic risks associated with CRISPR-Cas9, such as chromosomal translocations, p53-mediated cell cycle arrest, and elevated mutagenesis, making it safer for therapeutic applications in both dividing and non-dividing cells.^[27] This DSB-free mechanism also eliminates the toxicity linked to persistent breaks, reducing the potential for oncogenic transformations and improving overall cellular viability during editing.^[27]

Limitations

Prime editing, while promising for precise genome modifications, faces several key limitations that hinder its widespread application. Efficiency remains a primary challenge, with editing rates typically ranging from 10% to 50% in cultured cells such as HEK293T for standard prime editors like PE2 and PE3, though advanced variants can achieve higher rates up to 80% in optimized conditions.^[28] In vivo, efficiencies vary, often 10-30% but up to 50% or more in optimized mouse models for liver or brain tissues, though lower for complex edits such as insertions or multi-base substitutions due to factors like tissue accessibility and immune responses.^[28] This variability is exacerbated by pegRNA instability, where the reverse transcriptase template in the pegRNA is prone to degradation, limiting the tool's ability to facilitate large-scale changes beyond short insertions or deletions.^[28] Off-target effects, although lower than those of traditional Cas9 editing (which can reach 4-48% at endogenous loci), are still present in prime editing at rates of 0.1% to 2.2% in HEK293T cells, including unintended RT bystander editing where nearby non-target bases are altered during reverse transcription.^[28] These off-target events are harder to predict than Cas9 indels because they arise from reverse transcription errors rather than nuclease cleavage, complicating safety assessments for therapeutic use.^[2] Recent 2025 studies highlight cell-type dependent efficiency, with high performance in proliferative cells like HEK293T (up to 50%) but substantially lower rates in primary stem cells or non-dividing tissues (often <20%), underscoring the lack of a universal solution for diverse cellular contexts.^[29] The large size of prime editors, approximately twice that of Cas9 at over 6.5 kb for the core fusion protein (nCas9-RT), poses significant delivery challenges, exceeding the packaging limit of adeno-associated virus (AAV) vectors (~4.7 kb) and necessitating split systems that further reduce efficiency.^[28] Reliable editing is generally limited to alterations of about 80 nucleotides, with longer edits like insertions beyond this threshold suffering from decreased precision and yield due to flap resolution constraints in the cell's repair machinery.^[2] Additionally, prime editing exhibits no universal fix for challenging genomic regions with specific sequence motifs or low accessibility, where efficiency can vary due to factors like reverse transcription fidelity, as noted in 2025 analyses of variant performance across motifs. Recent 2025 advancements, including PE6 with optimized Cas9/RT variants and PE7 using pegRNA stabilization proteins, have improved efficiency in diverse cell types, while miniature editors like those based on TnpB or IscB mitigate delivery issues.^[29]

Delivery and implementation

Delivery methods

Prime editing components, consisting of the prime editor protein (typically a Cas9 nickase fused to a reverse transcriptase) and prime editing guide RNA (pegRNA), require effective delivery systems to achieve therapeutic potential in target cells. Viral vectors remain a primary modality due to their ability to transduce a wide range of cell types with high efficiency. Adeno-associated virus (AAV) vectors are particularly suited for in vivo applications, such as liver targeting, owing to their low immunogenicity and tropism for hepatocytes, though their packaging capacity is limited to approximately 4.7 kb, necessitating strategies to accommodate the larger size of prime editors.^[30]^[31] Lentiviral vectors, in contrast, are favored for ex vivo editing of dividing cells like hematopoietic stem cells, enabling stable integration and long-term expression of the editing machinery without the size constraints of AAV.^[32] These vectors have been employed to deliver prime editing ribonucleoproteins (RNPs) or plasmids into CD34+ cells, facilitating precise corrections in immune disorders.^[32] Non-viral delivery methods offer advantages in avoiding genomic integration and immune responses associated with viruses. Lipid nanoparticles (LNPs) have emerged as a promising approach for in vivo and ex vivo delivery of prime editor mRNA and pegRNA, achieving targeted editing in tissues like the liver through encapsulation and endosomal escape mechanisms.^[33] For in vitro applications, electroporation provides a straightforward, non-viral method to introduce RNPs or mRNA into cultured cells, with high transfection rates in primary and immortalized lines.^[34] In clinical contexts, delivery challenges are evident, as seen in the 2025 Phase 1/2 trial of PM359 for chronic granulomatous disease (CGD), where ex vivo transduction of patient-derived CD34+ hematopoietic stem cells using lentiviral vectors restored NADPH oxidase function in edited cells, though preexisting immunity to Cas9 posed risks of inflammatory responses. Initial data from the first patient showed 58% DHR positivity by day 15 and 66% by day 30; additional data from the second patient released in August 2025 demonstrated consistent rapid engraftment with 70% restoration of function in neutrophils by day 15.^[19]^[22]^[35] To address AAV's size limitations for prime editors exceeding 4.7 kb, dual-AAV splitting strategies divide the editor into two vectors—one encoding the N-terminal Cas9 nickase and the other the C-terminal reverse transcriptase—allowing co-delivery and reconstitution in vivo.^[30] In mouse models, such dual-AAV systems have demonstrated delivery efficiencies of up to 40% in liver and brain tissues, enabling therapeutically relevant editing without significant off-target effects.^[30]

Optimization strategies

Prime editing efficiency can be substantially enhanced through optimized design of prime editing guide RNAs (pegRNAs), which consist of a spacer sequence, a reverse transcriptase template (RTT), and a primer binding site (PBS). Tools such as PrimeDesign, introduced in 2020, facilitate rapid pegRNA and nicking sgRNA selection by evaluating on-target efficiency, off-target potential, and structural features like PBS and RTT lengths to maximize editing outcomes.^[36] Similarly, pegIT, a web-based tool, automates pegRNA design for user-defined edits across genomes, prioritizing PBS/RTT combinations that minimize secondary structures and improve binding stability.^[13] Engineered pegRNAs (epegRNAs) incorporate motifs like MS2 or boxB hairpins to recruit stabilizing proteins, extending pegRNA longevity and boosting editing efficiency by 3-4-fold in various cell types through reduced degradation and enhanced Cas9 association.^[37] Tuning PBS length is a key strategy, with shorter PBS (e.g., 10-13 nucleotides) often increasing efficiency 2-3-fold compared to longer variants by alleviating auto-inhibitory interactions between the RTT and PBS, thereby promoting more effective reverse transcription.^[38] In the PE3 system, which employs paired nicking with an additional sgRNA on the non-edited strand, indel formation via non-homologous end joining (NHEJ) is reduced by up to 50-70% relative to PE2, as the nick directs repair toward the edited strand and suppresses error-prone pathways. Cellular engineering approaches further refine prime editing by modulating DNA repair and checkpoint responses. Inhibiting NHEJ with SCR7, a DNA ligase IV antagonist, favors precise editing by limiting competing repair mechanisms that could disrupt the single-strand template, enhancing overall fidelity in prime editing contexts similar to traditional CRISPR applications.^[39] Transient suppression of p53 using inhibitors like i53 or dominant-negative p53 fragments (p53DD) mitigates cell cycle arrest triggered by editing-induced DNA damage, increasing prime editing efficiency by 2-5-fold across multiple loci without compromising cell viability.^[40] Recent advances incorporate machine learning to predict and optimize edit outcomes. In 2025, models like PrimeNet integrate chromatin accessibility and DNA methylation data to rationally design pegRNAs, achieving up to 80% accuracy in forecasting efficiency for diverse genomic contexts and outperforming rule-based tools.^[41] These AI-driven strategies prioritize high-impact features like open chromatin states, reducing trial-and-error in experimental design.

Applications

Research applications

Prime editing has emerged as a powerful tool for engineering model organisms, enabling precise insertions such as knock-in of fluorescent tags to study developmental genes. In zebrafish, researchers demonstrated efficient somatic editing using ribonucleoprotein complexes, achieving mutation frequencies up to 30% in embryos without requiring viral delivery, which facilitates rapid functional studies of gene expression during development.^[42] Similarly, in mice, upgraded prime editor systems have supported high-efficiency knock-ins and knockouts in zygotes, allowing the creation of animal models that recapitulate human genetic variations in developmental pathways.^[43] These applications leverage prime editing's ability to perform allele-specific modifications, targeting only mutant alleles while preserving wild-type sequences, as enhanced by strategies like ProPE that reduce off-target effects.^[44] In plant research, prime editing has been applied to modify genomes for agronomic traits without the indels associated with traditional CRISPR methods.^[45] This precision is particularly valuable for staple crops, where off-target edits could compromise food security. Prime editing supports functional genomic screens through high-throughput mutagenesis in cell lines, accelerating the discovery of gene functions and regulatory elements. The PRIME method, a pooled prime editing screen, enables the characterization of thousands of variants at single-base resolution in human cell lines, identifying essential nucleotides in enhancers across cancer contexts.^[46] Another platform uses synthetic prime editing sensors to evaluate genetic variants endogenously, revealing context-dependent chromatin effects and aiding in the annotation of non-coding regions.^[47] Notable examples include the editing of over 100 human disease-associated loci in induced pluripotent stem cells (iPSCs) via pooled approaches, generating isogenic lines to model polygenic disorders like type 2 diabetes.^[48] In viral genome engineering, prime editing has been used to modify SARS-CoV-2 spike protein sequences, creating variants to dissect entry mechanisms and host interactions.^[49] By 2025, prime editing has been adopted in numerous research publications, underscoring its versatility in basic science.

Therapeutic applications

Prime editing holds significant promise for treating monogenic diseases by enabling precise correction of pathogenic mutations without double-strand breaks, potentially addressing a broad spectrum of genetic disorders. In sickle cell disease, prime editing has demonstrated efficient ex vivo correction of the HBB gene mutation in patient-derived hematopoietic stem cells, achieving editing efficiencies of 15-41% and restoring wild-type hemoglobin production.^[50] Similarly, for cystic fibrosis, optimized prime editing systems have corrected the common CFTR F508del mutation in human airway epithelial cells with up to 60% efficiency, restoring chloride channel function and mucociliary clearance in preclinical models.^[51] In chronic granulomatous disease (CGD), prime editing targeting CYBB mutations in X-linked forms has shown preclinical success, with a 2025 Phase 1/2 clinical trial reporting safety and initial efficacy in restoring NADPH oxidase activity in edited patient cells.^[19] For neurological disorders, prime editing has been applied to correct mutations in mouse models, such as those causing alternating hemiplegia of childhood, restoring function in preclinical studies as of 2025.^[52] In oncology, prime editing facilitates the restoration of tumor suppressor function, such as reverting TP53 point mutations like L194F in breast cancer cell lines (as demonstrated in 2022), which reactivates p53-mediated apoptosis and inhibits tumor growth without off-target effects.^[53] Prime Medicine's clinical pipeline targets monogenic diseases, including CGD, Wilson's disease, and alpha-1 antitrypsin deficiency, leveraging ex vivo editing for blood disorders like CGD and in vivo delivery via lipid nanoparticles for liver-targeted therapies as of 2025.^[54] Overall, prime editing's versatility allows it to potentially correct up to 89% of known disease-associated genetic variants, expanding therapeutic reach beyond current CRISPR limitations. Early clinical data from ongoing trials underscore its safety profile in humans.

Emerging uses

Prime editing has shown promise in addressing structural variants, such as inversions and duplications, which are implicated in various chromosomal diseases. The prime editing inversion (PIE) system, developed in 2025, enables precise inversions of large genomic segments up to megabase scale without double-strand breaks, facilitating the correction of complex rearrangements.^[11] In synthetic biology, prime editing supports the construction of genetic circuits in bacteria by enabling precise, scarless modifications. A 2025 study optimized prime editing in probiotic Escherichia coli Nissle 1917, allowing multiplexed insertions and deletions to engineer synthetic circuits for controlled gene expression and pathway regulation.^[55] This approach has been used to redesign metabolic pathways, such as enhancing biofuel production.^[56] Twin prime editing (twinPE), an advanced variant, extends insertion capabilities beyond standard prime editing, enabling larger genomic inserts. In bacterial systems, twinPE facilitated the integration of synthetic modules for circuit engineering. Agricultural applications of prime editing include engineering crop resistance to viruses. Environmental uses extend to microbiome engineering, with prime editing applied in bacteria to modulate metabolic pathways.

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[6]
Engineered pegRNAs improve prime editing efficiency - Nature
Oct 4, 2021 · The resulting engineered pegRNAs (epegRNAs) improve prime editing efficiency 3–4-fold in HeLa, U2OS and K562 cells and in primary human fibroblasts without ...
[7]
Programmable deletion, replacement, integration and inversion of ...
Dec 9, 2021 · Here we describe twin prime editing (twinPE), a DSB-independent method that uses a prime editor protein and two prime editing guide RNAs (pegRNAs)Missing: pegRNAs | Show results with:pegRNAs
[8]
Development of a versatile nuclease prime editor with upgraded ...
Jan 19, 2023 · The applicability of nuclease-based form of prime editor (PEn) has been hindered by its complexed editing outcomes.
[9]
Prime editing-based tool enables precise genomic inversions at kilobase to chromosomal scale - Nature Chemical Biology
### Summary of PIE from https://www.nature.com/articles/s41589-025-02073-1
[10]
Battle brews among biotechs over next-gen gene editing tools
Mar 1, 2023 · Prime editing was quickly picked up by hundreds of outside labs, and spawned another billion-dollar company called Prime Medicine. She stood ...
[11]
pegIT - a web-based design tool for prime editing - Oxford Academic
Jun 1, 2021 · pegIT is a freely available, user-friendly web tool that allows for easy and efficient pegRNA design for numerous, including large-scale, user-defined edits.
[12]
Prime editing: Mechanism insight and recent applications in plants
Oct 4, 2023 · In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties.Rna-Dependent Dna... · Pe Applications In Plants · Long Dna Sequence...<|control11|><|separator|>
[13]
Prime editing using paired pegRNAs targeting NG- or NGG-PAM in ...
Prime editing (PE) enables precise genome modification, i.e., all 12 types of base substitution, as well as designed insertion and deletion.
[14]
News Release Details - Prime Medicine
Oct 24, 2024 · Prime Medicine is advancing a liver-directed Prime Editor program that aims to correct mutations in ATP7B to restore copper metabolism.
[15]
[PDF] Development of PM359, a Prime Edited CD34+ cell drug product for ...
• Prime Medicine has Received FDA Clearance of Investigational New Drug (IND) Application for PM359 for the Treatment of Chronic Granulomatous Disease (CGD).Missing: trial | Show results with:trial
[16]
Prime Medicine Announces FDA Clearance of Investigational New ...
Apr 29, 2024 · The US Food and Drug Administration (FDA) has cleared the company's Investigational New Drug (IND) application for PM359, submitted on March 29, for the ...Missing: EMEA track
[17]
Prime Medicine Announces Breakthrough Clinical Data Showing ...
May 19, 2025 · Prime Medicine Announces Breakthrough Clinical Data Showing Rapid Restoration of DHR Positivity After Single Infusion of PM359, an ...
[18]
First-Ever Prime-Editing Therapy Shows Safety and Efficacy in ...
May 21, 2025 · In May 2024, Prime Medicine announced that the FDA had cleared its IND application for PM359 for the treatment of CGD, making PM359 the first ...
[19]
Engineered prime editors with minimal genomic errors - Nature
Sep 17, 2025 · A prime editor comprises a Cas9 nickase (Cas9n) fused to a reverse transcriptase and paired with an extended guide RNA (pegRNA) that encodes ...<|control11|><|separator|>
[20]
CRISPR Clinical Trials: A 2025 Update - Innovative Genomics Institute
Jul 9, 2025 · An update on the progress of CRISPR clinical trials with the latest data and a survey of the CRISPR landscape in 2025.
[21]
Methodologies for Improving HDR Efficiency - Frontiers
Results showed that HDR efficiency was enhanced from 5 to 8–14% when transfected with single shRNAs against KU70, KU80, or DNA ligase IV.Abstract · NHEJ Pathway · HDR Pathway · Favoring the HDR Pathway...
[22]
Prime Editing, a Novel Genome-Editing Tool That May Surpass ...
Prime Editing (PE) is a site-specific mutagenesis approach developed 2 years ago for highly precise and efficient genome editing.Prime Editing Might Be The... · Prime Editing Generations · Prime Editing In Cancer...<|separator|>
[23]
Prime editing: therapeutic advances and mechanistic insights - Nature
Nov 28, 2024 · A big part of the appeal of prime editing is its ability to precisely edit DNA without double stranded breaks, and to install any of the 12 possible single- ...Pegrna Design Tools · Paired Pegrna Systems · Mismatch Repair Modifiers...
[24]
https://innovativegenomics.org/news/crispr-clinical-trials-2025/
[25]
https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2018.00691/full
[26]
Efficient prime editing in mouse brain, liver and heart with dual AAVs
May 4, 2023 · The resulting dual-AAV systems, v1em and v3em PE-AAV, enable therapeutically relevant prime editing in mouse brain (up to 42% efficiency in cortex), liver (up ...
[27]
Prime Editing: An All-Rounder for Genome Editing - PMC - NIH
Aug 30, 2022 · A range of viral vectors have been used to deliver genome editing tools, including adeno-associated viral (AAV), lentiviral, retroviral, ...
[28]
Lentiviral Vectors for Delivery of Gene-Editing Systems Based on ...
Lentiviral vector (LV) systems are one of the main delivery vehicles for the CRISPR/Cas systems due to (i) its ability to carry bulky and complex transgenes.
[29]
Safer and efficient base editing and prime editing via ... - Nature
Nov 28, 2024 · The current standard for delivery of gene therapy and gene editing constructs is via viral vectors. However, the net size of the guide RNA ...
[30]
Prime editing in mammals: From promise to practicalities - PMC
The most common delivery methods are electroporation, viral delivery ... non-viral delivery approaches such as LNPs and eVLPs are becoming increasingly desirable.
[31]
PrimeDesign software for rapid and simplified design of prime ... - NIH
Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA ( ...
[32]
Engineered pegRNAs improve prime editing efficiency - PMC - NIH
We found that pegRNAs were degraded to a greater extent from this treatment compared to epegRNAs (1.9-fold compared to evopreQ1 and 1.8-fold compared to mpknot, ...
[33]
Reducing the inherent auto-inhibitory interaction within the pegRNA ...
May 29, 2023 · Synthetic pegRNAs with shorter PBS lengths increase prime editing efficiency of PE RNPs at endogenous loci. To examine the impact of the auto- ...Missing: tuning | Show results with:tuning<|separator|>
[34]
Ligase IV inhibitor SCR7 enhances gene editing directed ... - PubMed
The data of this study suggests that a combination of co-expression vector, ssODN, and ligase IV inhibitor can markedly improve the CRISPR/Cas9-directed gene ...Missing: prime | Show results with:prime
[35]
Transient inhibition of p53 enhances prime editing and cytosine ...
Oct 27, 2022 · Here we report that co-delivering of p53DD, a dominant negative fragment of p53, can greatly enhance prime editing and cytosine base editing efficiencies.
[36]
PrimeNet: rational design of Prime editing pegRNAs by deep learning
Jun 19, 2025 · This model integrates significant epigenetic factors, including chromatin accessibility and DNA methylation, which directly affect the ...
[37]
Revolutionizing CRISPR technology with artificial intelligence - Nature
Jul 31, 2025 · Based on results from in situ genome engineering, they generated the chromatin accessibility enabled learning model (CAELM), which integrates ...
[38]
CRISPR prime editing with ribonucleoprotein complexes ... - Synthego
Here we demonstrate prime editing with purified ribonucleoprotein complexes. We introduced somatic mutations in zebrafish embryos with frequencies as high as 30 ...
[39]
An upgraded nuclease prime editor platform enables high-efficiency ...
Jan 20, 2025 · An upgraded nuclease prime editor platform enables high-efficiency singled or multiplexed knock-in/knockout of genes in mouse and sheep zygotes ...
[40]
ProPE expands the prime editing window and enhances gene ...
Oct 10, 2025 · Prime editing (PE) is a promising gene editing method that exploits a reverse transcriptase fused to a Cas9, whose single guide RNA (sgRNA) ...
[41]
Prime Editing for Crop Improvement: A Systematic Review of ... - NIH
Aug 16, 2025 · Prime editing (PE), a novel “search-and-replace” genome editing technology, demonstrates significant potential for crop genetic improvement ...
[42]
High-throughput evaluation of genetic variants with prime editing ...
Mar 12, 2024 · Here we present a high-throughput prime editing sensor strategy that couples prime editing guide RNAs with synthetic versions of their cognate target sites.
[43]
Generation of Human Isogenic Induced Pluripotent Stem Cell Lines ...
Feb 14, 2024 · With attention to design, prime editing is a promising approach to generate isogenic iPSC lines, enabling the study of specific genetic changes ...
[44]
Prime editor‐mediated functional reshaping of ACE2 prevents the ...
Sep 10, 2023 · Prime editor‐mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS‐CoV‐2 variants.
[45]
Rewriting the script: gene therapy and genome editing for von ...
In hemophilia patients, siRNA targeting antithrombin has been studied extensively with the aim to restore the hemostatic balance. Patients treated with this ...
[46]
Precision engineering of the probiotic Escherichia coli Nissle 1917 ...
We present a streamlined prime editing approach tailored for probiotic Escherichia coli Nissle 1917 utilizing only essential genetic modules.
[47]
A versatile genetic engineering toolkit for E. coli based on CRISPR ...
Sep 1, 2021 · In summary, our results indicate a very high fidelity of CRISPR-Prime Editing system on both plasmid and chromosome DNA engineering in E. coli.
[48]
Prime Editing for Crop Improvement: A Systematic Review of ... - MDPI
Our analysis revealed that early PE systems such as PE2 could perform diverse edits, including all 12 base substitutions and small insertions or deletions ( ...
[49]
Therapeutic engineering of the gut microbiome using synthetic ... - NIH
Aug 6, 2025 · ... (2025) Precision engineering of the probiotic Escherichia coli Nissle 1917 with prime editing. Appl Environ Microbiol 91(2). 10.1128/aem ...<|control11|><|separator|>
[50]
Advances in large-scale DNA engineering with the CRISPR system
Sep 1, 2025 · The use of highly accurate, modular prime editing technologies could enable precise, large-scale genome editing. In addition, the CRISPR–Cas12f ...