Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e29 (2021).
Doman, J. L., Sousa, A. A., Randolph, P. B., Chen, P. J. & Liu, D. R. Designing and executing prime editing experiments in mammalian cells. Nat. Protoc. 17, 2431–2468 (2022).
Liu, P. et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat. Commun. 12, 2121 (2021).
Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402–410 (2022).
Li, X. et al. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat. Commun. 13, 1669 (2022).
Ponnienselvan, K. et al. Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency. Nucleic Acids Res. 51, 6966–6980 (2023).
Yarnall, M. T. N. et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2023).
Grunewald, J. et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat. Biotechnol. 41, 337–343 (2023).
Feng, Y. et al. Enhancing prime editing efficiency and flexibility with tethered and split pegRNAs. Protein Cell 14, 304–308 (2023).
Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002.e26 (2023).
Liu, B. et al. Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nat. Biotechnol. 42, 1039–1045 (2023).
da Silva, J. F. et al. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02324-x (2024).
Petri, K. et al. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat. Biotechnol. 40, 189–193 (2022).
Davis, J. R. et al. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat. Biotechnol. 42, 253–264 (2023).
Diamond, T. L. et al. Macrophage tropism of HIV-1 depends on efficient cellular dNTP utilization by reverse transcriptase. J. Biol. Chem. 279, 51545–51553 (2004).
Gao, W. Y., Cara, A., Gallo, R. C. & Lori, F. Low levels of deoxynucleotides in peripheral blood lymphocytes: a strategy to inhibit human immunodeficiency virus type 1 replication. Proc. Natl Acad. Sci. USA 90, 8925–8928 (1993).
Hakansson, P., Hofer, A. & Thelander, L. Regulation of mammalian ribonucleotide reduction and dNTP pools after DNA damage and in resting cells. J. Biol. Chem. 281, 7834–7841 (2006).
Traut, T. W. Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem. 140, 1–22 (1994).
Skasko, M. et al. Mechanistic differences in RNA-dependent DNA polymerization and fidelity between murine leukemia virus and HIV-1 reverse transcriptases. J. Biol. Chem. 280, 12190–12200 (2005).
Oscorbin, I. P. & Filipenko, M. L. M-MuLV reverse transcriptase: selected properties and improved mutants. Comput. Struct. Biotechnol. J. 19, 6315–6327 (2021).
Paliksa, S., Alzbutas, G. & Skirgaila, R. Decreased Km to dNTPs is an essential M-MuLV reverse transcriptase adoption required to perform efficient cDNA synthesis in one-step RT–PCR assay. Protein Eng. Des. Sel. 31, 79–89 (2018).
Kaushik, N., Chowdhury, K., Pandey, V. N. & Modak, M. J. Valine of the YVDD motif of moloney murine leukemia virus reverse transcriptase: role in the fidelity of DNA synthesis. Biochemistry 39, 5155–5165 (2000).
Operario, D. J., Reynolds, H. M. & Kim, B. Comparison of DNA polymerase activities between recombinant feline immunodeficiency and leukemia virus reverse transcriptases. Virology 335, 106–121 (2005).
Ni, P. et al. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biol. 24, 156 (2023).
Halperin, S.O. Methods and compositions for directed genome editing. US patent 20230076357A1 (2023).
Das, D. & Georgiadis, M. M. A directed approach to improving the solubility of Moloney murine leukemia virus reverse transcriptase. Protein Sci. 10, 1936–1941 (2001).
Liang, S. Q. et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat. Methods 20, 898–907 (2023).
Guo, D. et al. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling. eLife 11, e70341 (2022).
Mathews, C. K. Deoxyribonucleotide metabolism, mutagenesis and cancer. Nat. Rev. Cancer 15, 528–539 (2015).
Goldstone, D. C. et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature 480, 379–382 (2011).
Laguette, N. et al. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by VPX. Nature 474, 654–657 (2011).
Deutschmann, J. & Gramberg, T. SAMHD1 … and viral ways around it. Viruses 13, 395 (2021).
Bergamaschi, A. et al. The human immunodeficiency virus type 2 VPX protein usurps the CUL4A–DDB1 DCAF1 ubiquitin ligase to overcome a postentry block in macrophage infection. J. Virol. 83, 4854–4860 (2009).
Srivastava, S. et al. Lentiviral VPX accessory factor targets VprBP/DCAF1 substrate adaptor for cullin 4 E3 ubiquitin ligase to enable macrophage infection. PLoS Pathog. 4, e1000059 (2008).
Hrecka, K. et al. VPX relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474, 658–661 (2011).
Korin, Y. D. & Zack, J. A. Nonproductive human immunodeficiency virus type 1 infection in nucleoside-treated G0 lymphocytes. J. Virol. 73, 6526–6532 (1999).
Meyerhans, A. et al. Restriction and enhancement of human immunodeficiency virus type 1 replication by modulation of intracellular deoxynucleoside triphosphate pools. J. Virol. 68, 535–540 (1994).
Plesa, G. et al. Addition of deoxynucleosides enhances human immunodeficiency virus type 1 integration and 2LTR formation in resting CD4+ T cells. J. Virol. 81, 13938–13942 (2007).
Chabes, A. & Stillman, B. Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 104, 1183–1188 (2007).
Pajalunga, D. et al. A defective dNTP pool hinders DNA replication in cell cycle-reactivated terminally differentiated muscle cells. Cell Death Differ. 24, 774–784 (2017).
Sawa, C. et al. High concentration of extracellular nucleotides suppresses cell growth via delayed cell cycle progression in cancer and noncancer cell lines. Heliyon 7, e08318 (2021).
Wakade, A. R., Przywara, D. A., Palmer, K. C., Kulkarni, J. S. & Wakade, T. D. Deoxynucleoside induces neuronal apoptosis independent of neurotrophic factors. J. Biol. Chem. 270, 17986–17992 (1995).
Purhonen, J., Banerjee, R., McDonald, A. E., Fellman, V. & Kallijarvi, J. A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase. Nucleic Acids Res. 48, e87 (2020).
Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40, 731–740 (2022).
Nishimasu, H. et al. Engineered CRISPR–Cas9 nuclease with expanded targeting space. Science 361, 1259–1262 (2018).
Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273, 1856–1862 (1996).
Liu, R. et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86, 367–377 (1996).
Samson, M. et al. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722–725 (1996).
Pagliuca, F. W. et al. Generation of functional human pancreatic β cells in vitro. Cell 159, 428–439 (2014).
Rezania, A. et al. Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells. Nat. Biotechnol. 32, 1121–1133 (2014).
Philippe, C. et al. Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update. Eur. J. Med. Genet. 49, 9–18 (2006).
Kerem, B. S. et al. Identification of mutations in regions corresponding to the two putative nucleotide (ATP)-binding folds of the cystic fibrosis gene. Proc. Natl Acad. Sci. USA 87, 8447–8451 (1990).
Myerowitz, R. & Costigan, F. C. The major defect in Ashkenazi Jews with Tay–Sachs disease is an insertion in the gene for the α-chain of β-hexosaminidase. J. Biol. Chem. 263, 18587–18589 (1988).
Levesque, S., Cosentino, A., Verma, A., Genovese, P. & Bauer, D. E. Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02266-4 (2024).
Madigan, V., Zhang, F. & Dahlman. J. E. Drug delivery systems for CRISPR-based genome editors. Nat. Rev. Drug Discov. 22, 875–894 (2023).
Hopfner, K.-P. & Hornung, V. Molecular mechanisms and cellular functions of cGAS–STING signalling. Nat. Rev. Mol. Cell Biol. 21, 501–521 (2020).
Dumousseau, M., Rodriguez, N., Juty, N. & Le Novere, N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics 13, 101 (2012).
Guo, D., Daman, K., Durso, D. F., Yan, J. & Emerson, C. P. Generation of iMyoblasts from human induced pluripotent stem cells. Bio Protoc. 12, e4500 (2022).
Veres, A. et al. Charting cellular identity during human in vitro β-cell differentiation. Nature 569, 368–373 (2019).
Balboa, D. et al. Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells. Nat. Biotechnol. 40, 1042–1055 (2022).
Baiersdorfer, M. et al. A facile method for the removal of dsRNA contaminant from in vitro-transcribed mRNA. Mol. Ther. Nucleic Acids 15, 26–35 (2019).
Sabnis, S. et al. A novel amino lipid series for mRNA delivery: improved endosomal escape and sustained pharmacology and safety in non-human primates. Mol. Ther. 26, 1509–1519 (2018).
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
Liu, P. et al. Increasing intracellular dNTP levels improves prime editing efficiency. Sequence Read Archive https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1024467 (2024).