Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Open accessAbstract
The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases. The deamination of adenine yields inosine, which is treated as guanine by polymerases, but no enzymes are known to deaminate adenine in DNA. Here we describe adenine base editors (ABEs) that mediate the conversion of A•T to G•C in genomic DNA. We evolved a transfer RNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9 mutant. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs that convert targeted A•T base pairs efficiently to G•C (approximately 50% efficiency in human cells) with high product purity (typically at least 99.9%) and low rates of indels (typically no more than 0.1%). ABEs introduce point mutations more efficiently and cleanly, and with less off-target genome modification, than a current Cas9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells. Together with previous base editors, ABEs enable the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.
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ABE generally does not induce double-strand breaks (<1%) and is therefore a favorable alternative to Cas9 for single and multiplex gene knockouts.
“Adenine base editor (ABE), first described in 2017, generally does not induce DSBs (<1%) and is therefore a favorable alternative to Cas9 for single and multiplex gene knockouts.12,14”
From Adenine base editor for knockout of proteins: A practical guide from design to analysis with updated MultiEditRbatch (2026) · cites this paper as [14]
The Results (Characterization of Late-Stage ABEs; page unavailable) report <0.1% indels with ABE7.10 at five tested loci and describe base editing without introducing double-strand breaks. They do not establish a measured <1% double-strand-break rate or evaluate ABE as an alternative to Cas9 for single or multiplex gene knockouts; the comparison with Cas9 concerns point mutations. (LLM, conf=0.88)
Experimental — accuracy not yet measuredTransition mutations occur significantly more often in human disease than transversion mutations (62% transition vs 38% transversion).
“Yet, these mutations occur significantly more often in human disease than transversion mutations (62% transition vs 38% transversion29,63).”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [29]
The Abstract (page not provided) says C•G-to-T•A transitions alone account for approximately half of known human pathogenic point mutations, supporting the general prominence of transitions in disease. It does not give the claimed 62% versus 38% breakdown or a statistical comparison with transversions. (LLM, conf=0.82)
Experimental — accuracy not yet measuredCBE converts cytosine to thymine.
“CBE converts cytosine to thymine”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Gaudelli et al., 2017
ABE 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 Gaudelli et al., 2017
Base 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 Gaudelli et al., 2017
Base 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 [13]
Fusing adenine deaminase to a nickase-Cas9 creates an ABE that mediates A > G base changes via an inosine intermediate.
“Fusing adenine deaminase (an evolved TadA heterodimer) to a nickase-Cas9 creates an adenine base editor (ABE) that mediates A > G base changes via an inosine intermediate29”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [29]
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 [49]
The Results section on disease-relevant mutations describes adenine base editing in human cells, including correction of an HFE mutation, not editing in mdx mice. Searches for mdx, exon 23, DMD, and dystrophin found no passage reporting mutation removal or dystrophin recovery in skeletal or cardiac muscle. Page numbers are unavailable in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredABE6.3 resulted in the highest A>G base editing efficiency at position A9 in Fah mutant mouse embryonic fibroblast cells (6.9 ± 2.0% with 2 μg ABE6.3).
“Consistent with the literature1, ABE6.3 resulted in the highest A>G base editing efficiency at position A9 (6.9 ± 2.0%,2 µg ABE6.3) (Supplementary Fig. 1) and editing efficiency was dependent of the ABE enzyme concentration.”
From Adenine base editing in an adult mouse model of tyrosinaemia (2019) · cites this paper as [1]
Adenine base editors comprise an evolved Escherichia coli TadA and Cas9 nickase and mediate A•T to G•C substitutions.
“Adenine BEs comprise an evolved Escherichia coli TadA (ecTadA*, a tRNA adenosine deaminase evolved to accept DNA substrate) and Cas9 nickase, and mediate A•T to G•C substitutions1.”
From Adenine base editing in an adult mouse model of tyrosinaemia (2019) · cites this paper as [1]
The ABE editing window occupies positions ~4-9 with the 1st, 5' nucleotide of the candidate sgRNA counted as position 1.
“The ABE editing window occupies positions ~4–9 with the 1st, 5’ nucleotide (nt) of the candidate sgRNA counted as position 1 1.”
From Adenine base editing in an adult mouse model of tyrosinaemia (2019) · cites this paper as [1]
Point mutations are a frequent cause of genetic disease, and approximately 50% of disease point mutations are G:C>A:T.
“Point mutations are a frequent cause of genetic disease, with ~50% of disease point mutations being G:C>A:T 1.”
From Adenine base editing in an adult mouse model of tyrosinaemia (2019) · cites this paper as [1]
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- Authors
- Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Liu, David R.
- ORCID
- Venue
- Nature
- Published
- 2017-11-01
- Volume
- 551
- Issue
- 7681
- Pages
- 464-471
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5726555
- OpenAlex
- W2766599608
- Cited by
- 4,184
- References
- 46
- Citations by year
- 2026: 460 · 2025: 501 · 2024: 521 · 2023: 599 · 2022: 557 · 2021: 489 · 2020: 474 · 2019: 332 · 2018: 237 · 2017: 8 · 2014: 1 · 2013: 1 · 2012: 1
- FWCI
- 117.56
- Type
- journal article
- Language
- en
- Update notices
- correction (2018-05-02)
- Open access
- green
- europepmc.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- 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 Human Genome Research Institute (RM1HG009490)
- National Institute of General Medical Sciences (T32GM008313, F32GM106621, R35GM118062, 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
- adenine base editors, base editing, cytosine deamination, CRISPR/Cas9, directed evolution, protein engineering, transition mutations, point mutations, single nucleotide polymorphisms
- MeSH terms
- Gene Editing, Adenosine Deaminase, DNA, Humans, Models, Molecular, Genome, Human, Base Pairing, Polymorphism, Single Nucleotide, Cell Line, Tumor, DNA Cleavage, HEK293 Cells, CRISPR-Associated Proteins
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