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Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

Nature volume 551, pages 464471 (23 November 2017) | Download Citation

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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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Change history

  • 02 May 2018

    Please see accompanying Publisher correction ( In this Article, owing to an error during the production process, in Fig. 1a, the dark blue and light blue wedges were incorrectly labelled as 'G•C  →  T•A' and 'G•C  → A•T', instead of 'C•G  → T•A' and 'C•G  → A•T', respectively. This error has been corrected online.


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  1. 1.

    , & Uracil in DNA—occurrence, consequences and repair. Oncogene 21, 8935–8948 (2002)

  2. 2.

    , , , & Cytosine deamination and the precipitous decline of spontaneous mutation during Earth’s history. Proc. Natl Acad. Sci. USA 113, 8194–8199 (2016)

  3. 3.

    , , , & Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016)

  4. 4.

    et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, aaf8729 (2016)

  5. 5.

    et al. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci. Adv. 3, eaao4774 (2017)

  6. 6.

    , & Editing the genome without double-stranded DNA breaks. ACS Chem. Biol. (2017)

  7. 7.

    et al. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol. 35, 371–376 (2017)

  8. 8.

    et al. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat. Commun. 8, 15790 (2017)

  9. 9.

    et al. Precise genome-wide base editing by the CRISPR Nickase system in yeast. Sci. Rep. 7, 2095 (2017)

  10. 10.

    & Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system. Mol. Plant 10, 523–525 (2017)

  11. 11.

    et al. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat. Biotechnol. 35, 438–440 (2017)

  12. 12.

    et al. Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system. Nat. Commun. 8, 118 (2017)

  13. 13.

    et al. CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Mol. Cell 67, 1068–1079 (2017)

  14. 14.

    et al. CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. Nat. Methods 14, 710–712 (2017)

  15. 15.

    et al. Highly efficient RNA-guided base editing in mouse embryos. Nat. Biotechnol. 35, 435–437 (2017)

  16. 16.

    , & In vivo base editing of PCSK9 (proprotein convertase subtilisin/kexin Type 9) as a therapeutic alternative to genome editing. Arterioscler. Thromb. Vasc. Biol. 37, 1741–1747 (2017)

  17. 17.

    et al. Correction of β-thalassemia mutant by base editor in human embryos. Protein Cell (2017)

  18. 18.

    et al. Highly efficient and precise base editing in discarded human tripronuclear embryos. Protein Cell 8, 776–779 (2017)

  19. 19.

    , & Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation. Nat. Commun. 8, 15939 (2017)

  20. 20.

    et al. Miscoding properties of 2′-deoxyinosine, a nitric oxide-derived DNA Adduct, during translesion synthesis catalyzed by human DNA polymerases. J. Mol. Biol. 377, 1015–1023 (2008)

  21. 21.

    , & DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA. Nucleic Acids Res. 45, 3369–3377 (2017)

  22. 22.

    et al. Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry 45, 6407–6416 (2006)

  23. 23.

    , & tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J. 21, 3841–3851 (2002)

  24. 24.

    et al. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat. Struct. Mol. Biol. 23, 426–433 (2016)

  25. 25.

    , & Recent advances in understanding and managing adenosine deaminase and purine nucleoside phosphorylase deficiencies. Curr. Opin. Allergy Clin. Immunol. 13, 630–638 (2013)

  26. 26.

    & An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286, 1146–1149 (1999)

  27. 27.

    DNA mismatch repair in eukaryotes and bacteria. J. Nucleic Acids 2010, 260512 (2010)

  28. 28.

    et al. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. 24, 131–139 (2017)

  29. 29.

    et al. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 309, 1534–1539 (2005)

  30. 30.

    , & Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat. Struct. Mol. Biol. 13, 153–159 (2006)

  31. 31.

    , , , & Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. Proc. Natl Acad. Sci. USA 97, 13573–13578 (2000)

  32. 32.

    et al. Endonuclease V cleaves at inosines in RNA. Nat. Commun. 4, 2271 (2013)

  33. 33.

    et al. Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature 533, 125–129 (2016)

  34. 34.

    et al. Genome-wide target specificities of CRISPR RNA-guided programmable deaminases. Nat. Biotechnol. 35, 475–480 (2017)

  35. 35.

    et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015)

  36. 36.

    et al. A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition. Nat. Med. 22, 987–990 (2016)

  37. 37.

    et al. KLF1 drives the expression of fetal hemoglobin in British HPFH. Blood 130, 803–807 (2017)

  38. 38.

    & HFE-associated hereditary hemochromatosis. Genet. Med. 11, 307–313 (2009)

  39. 39.

    et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 44, D862–D868 (2016)

  40. 40.

    et al. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature 533, 58–63 (2016)

  41. 41.

    et al. Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution. Nucleic Acids Res. 33, e117 (2005)

  42. 42.

    , & A system for the continuous directed evolution of biomolecules. Nature 472, 499–503 (2011)

  43. 43.

    , , & Precise and efficient scarless genome editing in stem cells using CORRECT. Nat. Protocols 12, 329–354 (2017)

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This work was supported by DARPA HR0011-17-2-0049, US NIH RM1 HG009490, R01 EB022376, and R35 GM118062, and HHMI. A.C.K. and D.I.B. were Ruth L. Kirchstein National Research Service Awards Postdoctoral Fellows (F32 GM 112366 and F32 GM106621, respectively). M.S.P. was an NSF Graduate Research Fellow and was supported by training grant T32 GM008313. We thank Z. Niziolek for technical assistance. N.M.G. thanks A. E. Martin for his encouragement.

Author information

Author notes

    • Alexis C. Komor
    • , Michael S. Packer
    •  & David I. Bryson

    Present addresses: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA (A.C.K.); Beam Therapeutics, 675 West Kendall Street, Cambridge, Massachusetts 02139, USA (M.S.P., D.I.B.).


  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Nicole M. Gaudelli
    • , Alexis C. Komor
    • , Holly A. Rees
    • , Michael S. Packer
    • , Ahmed H. Badran
    • , David I. Bryson
    •  & David R. Liu
  2. Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA

    • Nicole M. Gaudelli
    • , Alexis C. Komor
    • , Holly A. Rees
    • , Michael S. Packer
    • , Ahmed H. Badran
    • , David I. Bryson
    •  & David R. Liu
  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Nicole M. Gaudelli
    • , Alexis C. Komor
    • , Holly A. Rees
    • , Michael S. Packer
    • , Ahmed H. Badran
    • , David I. Bryson
    •  & David R. Liu


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N.M.G designed the research, performed all evolution experiments, conducted human cell experiments, analysed data, and wrote the manuscript. A.C.K assisted with experimental design and human cell experiments and analysed data. H.A.R. performed HDR and off-target experiments. M.S.P. performed computational data analyses and developed HTS processing scripts. A.H.B contributed to selection design and evolution strategy. D.I.B. assisted with cloning of late-stage ABEs. D.R.L designed and supervised the research and wrote the manuscript. All of the authors contributed to editing the manuscript.

Competing interests

N.M.G., A.C.K., and D.R.L. have filed patent applications on this work. D.R.L. is a consultant and co-founder of Editas Medicine, Beam Therapeutics, and Pairwise Plants, companies that use genome editing technologies.

Corresponding author

Correspondence to David R. Liu.

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