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What is CRISPR gene editing?

10 cited papers · March 16, 2026 · Powered by Researchly AI

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TL;DR

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing is a revolutionary technology derived from a bacterial immune defense mechanism…

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing is a revolutionary technology derived from a bacterial immune defense mechanism that has transformed modern biology.¹²The CRISPR-Cas9 system enables researchers to modify, regulate, or mark genomic loci across a wide variety of cells and organisms from all three domains of life, opening a new era in which genomic manipulation is no longer a bottleneck to experiments.¹

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Genome editing. The new frontier of genome engineering with CRISPR-Cas9.Doudna Jennifer A, Charpentier Emmanuelle2014Science (New York, N.Y.)

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The CRISPR tool kit for genome editing and beyondMazhar Adli2018Nature Communications

CRISPR-Cas9 Mechanism — The system consists of a Cas9 nuclease guided by a single-guide RNA (sgRNA) that base-pairs with a target DNA sequence, enabling Cas9 to recognize and cut that specific site, generating double-strand breaks (DSBs).

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The CRISPR/Cas9 system and its applications in crop genome editingAili Bao, David J. Burritt et al.2019Critical Reviews in Biotechnology

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Comparative analysis of lipid Nanoparticle-Mediated delivery of CRISPR-Cas9 RNP versus mRNA/sgRNA for gene editing in vitro and in vivo.Johanna Walther, Deja Porenta et al.2024European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V

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Genome Engineering Using the CRISPR-Cas9 SystemF. Ann Ran, Patrick D. Hsu et al.2013Nature Protocols

DNA Repair Pathways — After a double-strand break is introduced, cells repair it via two main mechanisms: Non-Homologous End Joining (NHEJ), which often results in gene knockouts through deletions or frameshift errors, and Homology-Directed Repair (HDR), which enables precise gene correction when a DNA template is provided.

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Precision gene editing: The power of CRISPR-Cas in modern geneticsJeong H. Joo, Soogene Lee et al.2025Molecular Therapy. Nucleic Acids

Guide RNA Programming — Cas9 can be easily reprogrammed to target new genomic sites simply by altering its guide RNA sequence, making sequence-specific gene editing several magnitudes easier than prior methods.

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Base Editing — An advanced variant fuses CRISPR-Cas9 with a cytidine deaminase enzyme to enable direct, irreversible conversion of one target DNA base into another without requiring double-stranded DNA cleavage or a donor template.

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Diagram

 [Guide RNA (sgRNA)]
 |
 v
 [Cas9 Protein] <--- Programmed to target specific DNA sequence
 |
 v
 [Target Genomic DNA]
 |
 DSB Introduced
 / \
 / \
 NHEJ HDR
 | |
 Gene Precise
 Knockout Correction

CRISPR-Cas9 offers several advantages over conventional gene-editing methods such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), including cost-effectiveness, flexibility, and ease of use.¹Beyond simple gene editing, the application of catalytically impaired inactive Cas9 (dCas9) now extends to gene regulation, epigenetic editing, chromatin engineering, and genomic imaging, exceeding the gene-editing functionality of wild-type Cas9.²For therapeutic delivery, CRISPR-Cas9 components can be packaged into non-viral delivery vehicles — such as lipid nanoparticles (LNPs) — in the form of plasmid DNA, mRNA/sgRNA, or a ribonucleoprotein (RNP) complex to protect them from degradation and deliver them to target tissues.³

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CRISPR/Cas9 technology as a potent molecular tool for gene therapy.Karimian Ansar, Azizian Khalil et al.2019Journal of cellular physiology

2

The CRISPR tool kit for genome editing and beyondMazhar Adli2018Nature Communications

3

Comparative analysis of lipid Nanoparticle-Mediated delivery of CRISPR-Cas9 RNP versus mRNA/sgRNA for gene editing in vitro and in vivo.Johanna Walther, Deja Porenta et al.2024European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V

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Despite its transformative potential, CRISPR-Cas9 faces significant challenges including efficient delivery to target tissues and safety concerns, which remain key barriers to widespread therapeutic application.¹Additionally, the NHEJ repair pathway, which is the more common cellular response to double-strand breaks, often results in unintended mutations such as deletions or frameshift errors rather than precise corrections.²

1

CRISPR/Cas9 technology as a potent molecular tool for gene therapy.Karimian Ansar, Azizian Khalil et al.2019Journal of cellular physiology

2

Precision gene editing: The power of CRISPR-Cas in modern geneticsJeong H. Joo, Soogene Lee et al.2025Molecular Therapy. Nucleic Acids

CRISPR-Cas9 is derived from a bacterial adaptive immune system and has revolutionized genome engineering across all domains of life.

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The system works by using a guide RNA to direct the Cas9 nuclease to a specific DNA target, where it introduces a double-strand break.

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Two DNA repair pathways — NHEJ and HDR — determine whether the outcome is a gene knockout or a precise correction.
CRISPR-Cas9 surpasses older tools like ZFNs and TALENs in cost, flexibility, and ease of use.
Advanced variants like base editors allow single-base changes without requiring double-strand DNA cleavage.

1

Genome editing. The new frontier of genome engineering with CRISPR-Cas9.Doudna Jennifer A, Charpentier Emmanuelle2014Science (New York, N.Y.)

2

The CRISPR tool kit for genome editing and beyondMazhar Adli2018Nature Communications

3

The CRISPR/Cas9 system and its applications in crop genome editingAili Bao, David J. Burritt et al.2019Critical Reviews in Biotechnology

4

CRISPR/Cas9 in Genome Editing and BeyondHaifeng Wang, Marie La Russa et al.2016Annual Review of Biochemistry

5

Genome Engineering Using the CRISPR-Cas9 SystemF. Ann Ran, Patrick D. Hsu et al.2013Nature Protocols

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"CRISPR-Cas9 off-target effects and strategies to improve specificity"
"Applications of CRISPR in human genetic disease therapy and clinical trials"
"Comparison of CRISPR delivery methods: viral vs. lipid nanoparticle approaches"

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