{"meta":{"source":"The CRISPR Atlas","url":"https://crispr2.2.25.209.181.nip.io/technologies/crispr-cas9"},"data":{"id":1,"kind":"technology","slug":"crispr-cas9","name":"CRISPR-Cas9","alt_names":["Cas9","SpCas9","CRISPR/Cas9","CRISPR Cas9"],"tagline":"A protein that can be programmed with a short RNA guide to find one specific sequence in a genome and cut it.","simple":"Think of your DNA as an enormous instruction manual with about three billion letters. CRISPR-Cas9 is a pair of molecular scissors that comes with a sticky note. You write a short address on the sticky note — about twenty letters long — and the scissors go and find the one place in the manual that matches, then cut. What happens next is up to the cell: it notices the cut and repairs it, and that repair is where the edit actually comes from.","summary":"CRISPR-Cas9 is an RNA-guided DNA endonuclease adapted from the adaptive immune system of bacteria. A single guide RNA carrying a ~20-nucleotide spacer directs the Cas9 protein to a complementary genomic sequence adjacent to a protospacer-adjacent motif (PAM; 5'-NGG-3' for Streptococcus pyogenes Cas9). Cas9 then generates a blunt double-strand break roughly three base pairs upstream of the PAM. The editing outcome is determined by the cell's repair pathway, not by Cas9 itself.","body":[{"h":"How it works, step by step","ol":["<b>A guide is designed.</b> Researchers pick a ~20-letter stretch of the target gene and synthesise a matching guide RNA.","<b>The guide loads into Cas9.</b> The RNA and the protein form a complex; on its own, neither does anything useful.","<b>The complex searches.</b> It samples the genome, checking for a short motif called the PAM. Without a PAM next to the target, Cas9 will not cut — which is a real constraint on where you can edit.","<b>The DNA unzips and is checked.</b> Where the guide matches, the two DNA strands separate and pair with the guide.","<b>Both strands are cut.</b> Two nuclease domains, RuvC and HNH, each cut one strand, producing a double-strand break.","<b>The cell repairs the break — and that is the edit.</b> Non-homologous end joining usually reseals it messily, inserting or deleting a few letters and often disabling the gene. If a repair template is supplied and the cell is dividing, homology-directed repair can copy in a precise new sequence instead."],"note":"The “scissors” analogy is useful but it hides the most important part: Cas9 does not edit anything. It breaks DNA. The cell's own repair machinery makes the change, which is why the same cut can produce different outcomes in different cells — and why disabling a gene is far easier than correcting one.","image":"tech-cas9","caption":"Cas9, guided by an RNA, holding a DNA strand at the point of a double-strand break."},{"h":"What it is good at","p":["Knocking a gene out is CRISPR-Cas9's strongest suit, and it is what almost every approved and late-stage clinical programme actually does. Messy repair after a cut reliably scrambles a short stretch of sequence, and a scrambled stretch usually means a broken gene. If the therapeutic goal is “stop this gene working” — as it is for the BCL11A enhancer in sickle cell disease — that is exactly what you want.","It is also unmatched as a research tool. Making a guide RNA is cheap and fast, which is why a technique published in 2012 was in laboratories worldwide within a year."]},{"h":"What it is bad at","p":["Precisely correcting a mutation is hard. Homology-directed repair only operates in dividing cells and is inefficient even then, so “change this exact letter back” is a much weaker capability than the public conversation about CRISPR usually implies. This limitation is the reason base editing and prime editing were invented.","Double-strand breaks also carry their own risks: large deletions, chromosomal rearrangements, loss of a whole chromosome arm, and activation of the p53 damage response. These are the specific hazards that nuclease-free approaches are trying to avoid."]},{"h":"Off-target editing","p":["A guide can tolerate mismatches, so Cas9 sometimes cuts at sites that resemble the target. Modern practice reduces this with better guide design, high-fidelity Cas9 variants, and delivery as a short-lived ribonucleoprotein rather than as DNA that keeps expressing.","It is measured, not assumed: methods such as GUIDE-seq and CIRCLE-seq map candidate off-target sites genome-wide, which are then sequenced deeply in the edited cells. Regulators expect that data."]},{"h":"How it gets into a body","p":["Two routes. <b>Ex vivo</b>: cells are taken out of the patient, edited in a facility, and returned — the approach behind Casgevy. It gives you control and lets you check the cells before infusing them, but it requires the patient to undergo conditioning chemotherapy first.","<b>In vivo</b>: the editor is delivered into the body directly, usually to the liver in a lipid nanoparticle. This is far simpler for the patient — an infusion rather than a transplant — but you cannot inspect the result before it happens, and reaching tissues other than the liver remains the field's central unsolved delivery problem."]}],"facts":[{"label":"Category","value":"RNA-guided nuclease"},{"note":"Jinek et al., Science","label":"First described as a programmable tool","value":"2012","source":"Science"},{"note":"Independently by the Zhang and Church laboratories","label":"First shown in human cells","value":"January 2013","source":"Science"},{"label":"Key scientists","value":"Jennifer Doudna, Emmanuelle Charpentier, Feng Zhang, George Church, Virginijus Šikšnys"},{"label":"What it edits","value":"DNA"},{"label":"Cuts both DNA strands?","value":"Yes — a blunt double-strand break"},{"label":"Typical edit","value":"Gene knockout via insertion/deletion; precise correction only with a template and in dividing cells"},{"label":"Sequence requirement","value":"A PAM (5'-NGG-3' for SpCas9) immediately after the target"},{"label":"Delivery methods","value":"Electroporation of ribonucleoprotein (ex vivo); lipid nanoparticles and AAV (in vivo)"},{"label":"Clinical status","value":"An approved medicine exists (Casgevy, 2023)"},{"label":"Nobel Prize","value":"Chemistry 2020, to Charpentier and Doudna","source":"The Nobel Foundation"}],"faq":[{"a":"No single person. CRISPR sequences were noticed in bacteria in 1987 by Yoshizumi Ishino's group, their function as bacterial immunity was worked out through the 2000s by researchers including Francisco Mojica, Rodolphe Barrangou and Philippe Horvath, and the demonstration that Cas9 could be programmed with a guide RNA to cut chosen DNA came from Jennifer Doudna and Emmanuelle Charpentier's groups with Virginijus Šikšnys publishing closely related work the same year. Use in human cells followed in 2013 from Feng Zhang's and George Church's laboratories. Patent rights have been litigated for over a decade and remain contested.","q":"Who invented CRISPR?"},{"a":"It is not one thing, so there is no single answer. One CRISPR-based medicine has been approved after clinical trials, which means regulators judged its benefits to outweigh its risks for a specific group of patients — not that the technique is safe in general. Known hazards include off-target edits, large deletions and chromosomal rearrangements at the cut site, immune responses to the editing proteins, and the serious toxicity of the conditioning chemotherapy used in ex vivo treatments. Long-term follow-up is required precisely because the changes are permanent.","q":"Is CRISPR safe?"},{"a":"It has produced dramatic benefit in specific blood disorders where switching one gene off is enough, and one such treatment is approved. That is a narrow foothold, not a general capability. Most genetic diseases would need a precise correction in a tissue we cannot yet reach efficiently, and for those, work remains preclinical.","q":"Can CRISPR cure genetic diseases?"},{"a":"Not as used in medicine. Approved and clinical uses are somatic: they change cells in one person's body and are not inherited. Editing embryos, eggs or sperm — germline editing, which would be heritable — is prohibited or unapproved for clinical use in most countries.","q":"Does CRISPR change your children?"}],"sources":[{"url":"https://www.science.org/doi/10.1126/science.1225829","year":2012,"title":"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity","publisher":"Science (Jinek et al.)"},{"url":"https://www.science.org/doi/10.1126/science.1231143","year":2013,"title":"Multiplex genome engineering using CRISPR/Cas systems","publisher":"Science (Cong et al.)"},{"url":"https://www.genome.gov/about-genomics/policy-issues/what-is-Genome-Editing","title":"What is genome editing?","publisher":"National Human Genome Research Institute"},{"url":"https://www.nobelprize.org/prizes/chemistry/2020/summary/","year":2020,"title":"The Nobel Prize in Chemistry 2020","publisher":"The Nobel Foundation"}],"tags":["DNA","cuts DNA","clinical"],"category":"Nuclease editing","status":"Approved","evidence":"Approved treatment","image":"tech-cas9","data":{"scores":{"maturity":5,"precision":3},"compare":{"cuts":"Yes — double-strand break","cargo":"Cas9 is large (~4.2 kb of coding sequence), which strains AAV packaging limits","edits":"DNA, both strands","risks":"Large deletions, chromosomal rearrangements, p53 activation, off-target cuts","delivery":"Well established: RNP electroporation ex vivo, lipid nanoparticles to liver in vivo","maturity":"Approved medicine; multiple Phase 3 programmes","precision":"High at the target site; off-target cutting is measurable and must be assayed","applications":"Gene knockout, research screens, ex vivo cell therapy"}},"sort":10,"author":"The CRISPR Atlas editorial team","reviewer":null,"updated":"2026-08-19","reviewed":null,"related":{"learn":[{"kind":"learn","slug":"how-crispr-works","name":"How CRISPR works, step by step","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/learn/how-crispr-works"},{"kind":"learn","slug":"what-guide-rna-does","name":"What guide RNA does","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/learn/what-guide-rna-does"},{"kind":"learn","slug":"what-is-crispr","name":"What is CRISPR?","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/learn/what-is-crispr"},{"kind":"learn","slug":"what-is-a-genome","name":"What is a genome?","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/learn/what-is-a-genome"},{"kind":"learn","slug":"what-is-base-editing","name":"What is base editing?","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/learn/what-is-base-editing"},{"kind":"learn","slug":"off-target-editing","name":"What off-target editing means","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/learn/off-target-editing"}],"disease":[{"kind":"disease","slug":"attr-amyloidosis","name":"ATTR Amyloidosis","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/attr-amyloidosis"},{"kind":"disease","slug":"beta-thalassemia","name":"Beta Thalassemia","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/beta-thalassemia"},{"kind":"disease","slug":"cancer","name":"Cancer","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/cancer"},{"kind":"disease","slug":"diabetes","name":"Diabetes","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/diabetes"},{"kind":"disease","slug":"hiv","name":"HIV","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/hiv"},{"kind":"disease","slug":"hereditary-angioedema","name":"Hereditary Angioedema","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/hereditary-angioedema"},{"kind":"disease","slug":"inherited-blindness","name":"Inherited Blindness","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/inherited-blindness"},{"kind":"disease","slug":"sickle-cell-disease","name":"Sickle Cell Disease","rel":"treats","url":"https://crispr2.2.25.209.181.nip.io/diseases/sickle-cell-disease"}],"gene":[{"kind":"gene","slug":"bcl11a","name":"BCL11A","rel":"edits","url":"https://crispr2.2.25.209.181.nip.io/genes/bcl11a"},{"kind":"gene","slug":"klkb1","name":"KLKB1","rel":"edits","url":"https://crispr2.2.25.209.181.nip.io/genes/klkb1"},{"kind":"gene","slug":"ttr","name":"TTR","rel":"edits","url":"https://crispr2.2.25.209.181.nip.io/genes/ttr"}],"treatment":[{"kind":"treatment","slug":"ctx112","name":"CTX112","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/ctx112"},{"kind":"treatment","slug":"casgevy","name":"Casgevy (exagamglogene autotemcel)","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/casgevy"},{"kind":"treatment","slug":"edit-101","name":"EDIT-101 (Brilliance)","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/edit-101"},{"kind":"treatment","slug":"edit-401","name":"EDIT-401","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/edit-401"},{"kind":"treatment","slug":"ux-hypoimmune-islets","name":"Hypoimmune islet cell therapy","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/ux-hypoimmune-islets"},{"kind":"treatment","slug":"lonvoguran-ziclumeran","name":"Lonvoguran ziclumeran (lonvo-z)","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/lonvoguran-ziclumeran"},{"kind":"treatment","slug":"nexiguran-ziclumeran","name":"Nexiguran ziclumeran (nex-z)","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/treatments/nexiguran-ziclumeran"}],"trial":[{"kind":"trial","slug":"climb-121","name":"A Safety and Efficacy Study Evaluating CTX001 in Subjects With Severe Sickle Cell Disease","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/clinical-trials/climb-121"},{"kind":"trial","slug":"upenn-nyces","name":"NY-ESO-1-Redirected CRISPR-Edited T Cells in Patients With Multiple Myeloma and Sarcoma","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/clinical-trials/upenn-nyces"}],"company":[{"kind":"company","slug":"arbor-biotechnologies","name":"Arbor Biotechnologies","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/companies/arbor-biotechnologies"},{"kind":"company","slug":"crispr-therapeutics","name":"CRISPR Therapeutics","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/companies/crispr-therapeutics"},{"kind":"company","slug":"editas-medicine","name":"Editas Medicine","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/companies/editas-medicine"},{"kind":"company","slug":"intellia-therapeutics","name":"Intellia 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Church","rel":"developed","url":"https://crispr2.2.25.209.181.nip.io/scientists/george-church"},{"kind":"scientist","slug":"jennifer-doudna","name":"Jennifer Doudna","rel":"developed","url":"https://crispr2.2.25.209.181.nip.io/scientists/jennifer-doudna"},{"kind":"scientist","slug":"rodolphe-barrangou","name":"Rodolphe Barrangou","rel":"developed","url":"https://crispr2.2.25.209.181.nip.io/scientists/rodolphe-barrangou"},{"kind":"scientist","slug":"virginijus-siksnys","name":"Virginijus Šikšnys","rel":"developed","url":"https://crispr2.2.25.209.181.nip.io/scientists/virginijus-siksnys"}],"paper":[{"kind":"paper","slug":"jinek-2012","name":"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity","rel":"about","url":"https://crispr2.2.25.209.181.nip.io/research/jinek-2012"},{"kind":"paper","slug":"barrangou-2007","name":"CRISPR provides acquired resistance against viruses in prokaryotes","rel":"about","url":"https://crispr2.2.25.209.181.nip.io/research/barrangou-2007"},{"kind":"paper","slug":"mojica-2005","name":"Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements","rel":"about","url":"https://crispr2.2.25.209.181.nip.io/research/mojica-2005"},{"kind":"paper","slug":"cong-2013","name":"Multiplex genome engineering using CRISPR/Cas systems","rel":"about","url":"https://crispr2.2.25.209.181.nip.io/research/cong-2013"},{"kind":"paper","slug":"mali-2013","name":"RNA-guided human genome engineering via Cas9","rel":"about","url":"https://crispr2.2.25.209.181.nip.io/research/mali-2013"}],"agriculture":[{"kind":"agriculture","slug":"gene-edited-crops","name":"Gene-edited crops","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/agriculture/gene-edited-crops"},{"kind":"agriculture","slug":"gene-edited-wheat","name":"Gene-edited wheat","rel":"uses","url":"https://crispr2.2.25.209.181.nip.io/agriculture/gene-edited-wheat"}],"comparison":[{"kind":"comparison","slug":"crispr-vs-gene-therapy","name":"CRISPR vs Gene Therapy","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/compare/crispr-vs-gene-therapy"},{"kind":"comparison","slug":"crispr-vs-base-editing","name":"CRISPR-Cas9 vs Base Editing","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/compare/crispr-vs-base-editing"},{"kind":"comparison","slug":"cas9-vs-cas12","name":"CRISPR-Cas9 vs Cas12","rel":"related","url":"https://crispr2.2.25.209.181.nip.io/compare/cas9-vs-cas12"}]}}}