Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
Open accessAbstract
Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. Although most genetic diseases arise from point mutations, current approaches to point mutation correction are inefficient and typically induce an abundance of random insertions and deletions (indels) at the target locus resulting from the cellular response to dsDNA breaks. Here we report the development of 'base editing', a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring dsDNA backbone cleavage or a donor template. We engineered fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not induce dsDNA breaks, and mediate the direct conversion of cytidine to uridine, thereby effecting a C→T (or G→A) substitution. The resulting 'base editors' convert cytidines within a window of approximately five nucleotides, and can efficiently correct a variety of point mutations relevant to human disease. In four transformed human and murine cell lines, second- and third-generation base editors that fuse uracil glycosylase inhibitor, and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favour desired base-editing outcomes, resulting in permanent correction of ~15-75% of total cellular DNA with minimal (typically ≤1%) indel formation. Base editing expands the scope and efficiency of genome editing of point mutations.
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CRISPR-Cas9 coupled to DNA editing enzymes can catalyze targeted A-to-G or C-to-T genomic sequence changes without inducing a DNA break, potentially reversing pathogenic single-nucleotide changes or disabling genes via stop codon introduction.
“An alternative approach is to use CRISPR-Cas9 coupled to DNA editing enzymes that catalyze targeted A-to-G or Cto-T genomic sequence changes without inducing a break in DNA, potentially reversing pathogenic single-nucleotide changes or disabling genes via the introduction of a stop codon 25,26 .”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [25]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredBase editors couple Cas9 nickases with nucleotide deaminases to achieve single nucleotide conversion without introducing DSBs.
“Base editors are one such tool, which couple Cas9 nickases with nucleotide deaminases to achieve single nucleotide conversion without introducing DSBs.”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Komor et al., 2016
The Abstract describes fusions of Cas9 and a cytidine deaminase that convert a target base without double-stranded DNA breaks. It also distinguishes the first-generation editor, BE1, which uses catalytically dead Cas9, from BE3, which uses a Cas9 nickase. Thus, the nickase description applies to BE3 but not to every base editor described in the paper. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe discovery of spontaneous hydrolytic deamination of cytosine converting C-G base pairs to T-A in humans highlighted the potential of base editing for direct base pair conversion without requiring double-strand breaks or homology repair templates.
“The discovery of spontaneous hydrolytic deamination of cytosine converting C-G base pairs to T-A in humans highlighted the potential of base editing for direct base pair conversion without requiring double-strand breaks or homology repair templates (Komor, et al., 2016).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Komor, et al., 2016
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredBase editors use cytidine or adenine deaminases fused to Cas9 to introduce single nucleotide variants without inducing double-stranded breaks.
“Next-generation CRISPR tools, such as base editors, use enzymes like cytidine or adenine deaminases fused to Cas9 to introduce single nucleotide variants (SNVs) without DSBs.12,13”
From Protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools (2024) · cites this paper as [12]
The paper’s Abstract reports cytidine deaminase–Cas9 fusions that make C→T (or G→A) substitutions without double-stranded DNA breaks. It does not report base editors using adenine deaminases, so that part of the cited sentence is not supported by this source. (LLM, conf=0.89)
Experimental — accuracy not yet measuredAlternatives to DNA cleavage-induced editing include base editing, prime editing, and CRISPRi/CRISPRa.
“Alternatives to DNA cleavage-induced editing include using CRISPR-Cas9 for direct chemical sequence alteration (base editing) 25,26 , providing RNA templates for gene alteration (prime editing) 27,28 , and for transcriptional control (CRISPR interference, CRISPRi; CRISPR activation, CRISPRa) 29,30 (Fig. 3).”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [25]
Experimental — accuracy not yet measured
CBE converts cytosine to thymine.
“CBE converts cytosine to thymine”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Komor et al., 2016
First-generation base editors had limitations such as low efficiency and base excision repair activity that reversed edits.
“First-generation base editors had limitations such as low efficiency and base excision repair (BER) activity that reversed edits (Komor et al., 2016).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Komor et al., 2016
Second-generation editors, such as APOBEC-XTEN-dCas9-UGI, added a uracil DNA glycosylase inhibitor to improve C-to-T conversion but still had <0.1% indel formation, limiting precision.
“Second-generation editors, such as APOBEC-XTEN-dCas9-UGI, added an uracil DNA glycosylase inhibitor (UGI) to improve C-to-T conversion (Komor et al., 2016) but still had <0.1% indel formation, limiting precision (Azameti and Dauda, 2021).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Komor et al., 2016
Fusion of a cytidine deaminase to a nickase-Cas9(D10A) protein results in a CBE that allows for C > T base changes via a uracil intermediate.
“Fusion of a cytidine deaminase (rAPOBEC1) to a partially inactive nickase-Cas9(D10A) protein results in a cytidine base editor (CBE) that allows for C > T base changes via a uracil intermediate28”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [28]
CRISPR-Cas9 removed a mutation in exon 23 in the mdx mouse model of DMD, providing partial recovery of functional dystrophin in skeletal myofibers and cardiac muscle.
“The second study used CRISPR-Cas9-mediated genome editing to remove a mutation in exon 23 in the mdx mouse model of DMD, providing partial recovery of functional dystrophin protein in skeletal myofibers and cardiac muscle 25,26,49 .”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [25]
The paper’s main text describes base editing of APOE4 in mouse astrocytes, and its Extended Data describe correction of APOE4 and p53 mutations in mammalian cells. Searches for mdx mice, exon 23, DMD, and dystrophin found no passage addressing mutation removal or dystrophin recovery in skeletal and cardiac muscle. The cited paper therefore does not verify this specific claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredABE catalyzes editing from adenine to guanine.
“ABE catalyzes the editing from adenine to guanine”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Komor et al., 2016
The Abstract describes BE1–BE3 as cytosine base editors, reporting C→U and C→T editing. Searches for ABE and adenine-to-guanine editing found no passage addressing that claim; the paper’s results for different editors do not contradict it. (LLM, conf=0.77)
Experimental — accuracy not yet measuredVariations on functional genomics methods allow evaluation of genes, regulatory elements, and genetic variants at increasing scale and resolution.
“Variations on these methods enable the functional evaluation of genes (via knockout screens124), regulatory elements (using CRISPR interference and CRISPR activation screens125,126), and genetic variants (base editors127) at increasing scale and resolution29.”
From A brief history of human disease genetics (2020) · cites this paper as [127]
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- Authors
- Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Liu, David R.
- Venue
- Nature
- Published
- 2016-04-20
- Volume
- 533
- Issue
- 7603
- Pages
- 420-424
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4873371
- OpenAlex
- W2336828812
- Cited by
- 5,437
- References
- 36
- Citations by year
- 2026: 564 · 2025: 660 · 2024: 664 · 2023: 719 · 2022: 681 · 2021: 614 · 2020: 540 · 2019: 408 · 2018: 338 · 2017: 182 · 2016: 61 · 2012: 1
- FWCI
- 171.45
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (T32GM008313, F32 GM 106601-2, F32GM106601, F32 GM 112366-2, R01GM065400, F32GM112366)
- National Institute of Biomedical Imaging and Bioengineering (R01EB022376)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- base editing, CRISPR/Cas9, cytidine deaminase, point mutation correction, Cas9 nickase, DNA repair, guide RNA, genome editing, human disease models
- MeSH terms
- APOBEC-1 Deaminase, RNA, Guide, CRISPR-Cas Systems, Animals, Base Sequence, Cell Line, Cytidine, Cytidine Deaminase, Deoxyribonuclease I, DNA, DNA Repair, Genetic Engineering, Humans, Templates, Genetic, Uridine, Genes, p53, Genome, Point Mutation, Mice, Uracil-DNA Glycosidase, Apolipoprotein E4, DNA Cleavage, INDEL Mutation, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, CRISPR-Associated Proteins
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