Home NATURALEZA Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases

Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases

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  • Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63, 633–646 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Shen, M. W. et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 563, 646–651 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nat. Biotechnol. 36, 765–771 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Leibowitz, M. L. et al. Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing. Nat. Genet. 53, 895–905 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kosicki, M. et al. Cas9-induced large deletions and small indels are controlled in a convergent fashion. Nat. Commun. 13, 3422 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alanis-Lobato, G. et al. Frequent loss of heterozygosity in CRISPR–Cas9-edited early human embryos. Proc. Natl Acad. Sci. USA 118, e2004832117 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. 52, 662–668 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Nat. Med. 24, 927–930 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ihry, R. J. et al. p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells. Nat. Med. 24, 939–946 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cullot, G. et al. CRISPR–Cas9 genome editing induces megabase-scale chromosomal truncations. Nat. Commun. 10, 1136 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cullot, G. et al. Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR–Cas9. Nat. Commun. 14, 4072 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Boutin, J. et al. CRISPR–Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells. Nat. Commun. 12, 4922 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tsai, H.-H. et al. Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR–Cas9-mediated genome editing. Nat. Commun. 14, 5183 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hustedt, N. & Durocher, D. The control of DNA repair by the cell cycle. Nat. Cell Biol. 19, 1–9 (2017).

    Article 
    CAS 

    Google Scholar
     

  • Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat. Cell Biol. 21, 1468–1478 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grünewald, J. et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569, 433–437 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zuo, E. et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364, 289–292 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park, S. & Beal, P. A. Off-target editing by CRISPR-guided DNA base editors. Biochemistry 58, 3727–3734 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, T. P., Newby, G. A. & Liu, D. R. Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat. Protoc. 16, 1089–1128 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Porto, E. M., Komor, A. C., Slaymaker, I. M. & Yeo, G. W. Base editing: advances and therapeutic opportunities. Nat. Rev. Drug Discovery 19, 839–859 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Halperin, S. O. et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 560, 248–252 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tou, C. J., Schaffer, D. V. & Dueber, J. E. Targeted diversification in the S. cerevisiae genome with CRISPR-guided DNA polymerase I. ACS Synth. Biol. 9, 1911–1916 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Long, M. et al. Directed evolution of ornithine cyclodeaminase using an EvolvR-based growth-coupling strategy for efficient biosynthesis of l-proline. ACS Synth. Biol. 9, 1855–1863 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gossing, M. et al. Multiplexed guide RNA expression leads to increased mutation frequency in targeted window using a CRISPR-guided error-prone DNA polymerase in Saccharomyces cerevisiae. ACS Synth. Biol. 12, 2271–2277 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nakade, S. et al. Frame editors for precise, template-free frameshifting. Preprint at https://doi.org/10.1101/2022.12.05.518807 (2022).

  • Yang, Q. et al. Phage DNA polymerase prevents on-target damage and enhances precision of CRISPR editing. Preprint at https://doi.org/10.1101/2023.01.10.523496 (2023).

  • Yoo, K. W., Yadav, M. K., Song, Q., Atala, A. & Lu, B. Targeting DNA polymerase to DNA double-strand breaks reduces DNA deletion size and increases templated insertions generated by CRISPR/Cas9. Nucleic Acids Res. 50, 3944–3957 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sharon, E. et al. Functional genetic variants revealed by massively parallel precise genome editing. Cell 175, 544–557.e16 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kong, X. et al. Precise genome editing without exogenous donor DNA via retron editing system in human cells. Protein Cell 12, 899–902 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao, B., Chen, S.-A. A., Lee, J. & Fraser, H. B. Bacterial retrons enable precise gene editing in human cells. CRISPR J. 5, 31–39 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, P. J. & Liu, D. R. Prime editing for precise and highly versatile genome manipulation. Nat. Rev. Genet. 24, 161–177 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Berdis, A. J. Mechanisms of DNA polymerases. Chem. Rev. 109, 2862–2879 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Johansson, E. & Dixon, N. Replicative DNA polymerases. Cold Spring Harb. Perspect. Biol. 5, a012799 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ponnienselvan, K. et al. Addressing the dNTP bottleneck restricting prime editing activity. Preprint at https://doi.org/10.1101/2023.10.21.563443 (2023).

  • Egli, M. & Manoharan, M. Chemistry, structure and function of approved oligonucleotide therapeutics. Nucleic Acids Res. 51, 2529–2573 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chandler, M. et al. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat. Rev. Microbiol. 11, 525–538 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lovendahl, K. N., Hayward, A. N. & Gordon, W. R. Sequence-directed covalent protein-DNA linkages in a single step using HUH-tags. J. Am. Chem. Soc. 139, 7030–7035 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tompkins, K. J. et al. Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Nucleic Acids Res. 49, 1046–1064 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aird, E. J., Lovendahl, K. N., St. Martin, A., Harris, R. S. & Gordon, W. R. Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template. Commun. Biol. 1, 54 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Klenow, H. & Overgaard-Hansen, K. Proteolytic cleavage of DNA polymerase from Escherichia coli B into an exonuclease unit and a polymerase unit. FEBS Lett. 6, 25–27 (1970).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR–Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34, 339–344 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, L. et al. Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J. Virol. 84, 1674–1682 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chandra, A., Hughes, T. R., Nugent, C. I. & Lundblad, V. Cdc13 both positively and negatively regulates telomere replication. Genes Dev. 15, 404–414 (2001).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Glustrom, L. W. et al. Single-stranded telomere-binding protein employs a dual rheostat for binding affinity and specificity that drives function. Proc. Natl Acad. Sci. USA 115, 10315–10320 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Smiley, A. T. et al. Watson–Crick base-pairing requirements for ssDNA recognition and processing in replication-initiating HUH endonucleases. mBio 14, e02587-22 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Lawyer, F. C. et al. High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5′ to 3′ exonuclease activity. Genome Res. 2, 275–287 (1993).

    Article 
    CAS 

    Google Scholar
     

  • Blanco, L. et al. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264, 8935–8940 (1989).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Esteban, J. A., Soengas, M. S., Salas, M. & Blanco, L. 3′ → 5′ exonuclease active site of phi 29 DNA polymerase. Evidence favoring a metal ion-assisted reaction mechanism. J. Biol. Chem. 269, 31946–31954 (1994).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thyme, S. B., Akhmetova, L., Montague, T. G., Valen, E. & Schier, A. F. Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nat. Commun. 7, 11750 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ponnienselvan, K. et al. Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency. Nucleic Acids Res. 51, 6966–6980 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, W. et al. Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions. eLife 12, RP90948 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402–410 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e29 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ferreira da Silva, J. et al. Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair. Nat. Commun. 13, 760 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lahue, R. S., Au, K. G. & Modrich, P. DNA mismatch correction in a defined system. Science 245, 160–164 (1989).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Su, S. S., Lahue, R. S., Au, K. G. & Modrich, P. Mispair specificity of methyl-directed DNA mismatch correction in vitro. J. Biol. Chem. 263, 6829–6835 (1988).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mathis, N. et al. Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02268-2 (2024).

  • Mathis, N. et al. Predicting prime editing efficiency and product purity by deep learning. Nat. Biotechnol. 41, 1151–1159 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002.e26 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Petri, K. et al. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat. Biotechnol. 40, 189–193 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Grünewald, J. et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat. Biotechnol. 41, 337–343 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Li, X. et al. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat. Commun. 13, 1669 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ricchetti, M. & Buc, H. E. coli DNA polymerase I as a reverse transcriptase. EMBO J. 12, 387–396 (1993).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krzywkowski, T., Kühnemund, M., Wu, D. & Nilsson, M. Limited reverse transcriptase activity of phi29 DNA polymerase. Nucleic Acids Res. 46, 3625–3632 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, D. Y., Moon, S. B., Ko, J.-H., Kim, Y.-S. & Kim, D. Unbiased investigation of specificities of prime editing systems in human cells. Nucleic Acids Res. 48, 10576–10589 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, Z. et al. PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation. Nat. Commun. 13, 7545 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liang, S.-Q. et al. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Nat. Commun. 13, 437 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bae, S., Park, J. & Kim, J.-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kamtekar, S. et al. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Mol. Cell 16, 609–618 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rodríguez, I. et al. A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity. Proc. Natl Acad. Sci. USA 102, 6407–6412 (2005).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • de Vega, M., Lázaro, J. M., Mencía, M., Blanco, L. & Salas, M. Improvement of φ29 DNA polymerase amplification performance by fusion of DNA binding motifs. Proc. Natl Acad. Sci. USA 107, 16506–16511 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Povilaitis, T., Alzbutas, G., Sukackaite, R., Siurkus, J. & Skirgaila, R. In vitro evolution of phi29 DNA polymerase using isothermal compartmentalized self replication technique. Protein Eng. Des. Sel. 29, 617–628 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ong, J., Tanner, N., Zhang, Y., Bei, Y. & Potapov, V. Variant DNA polymerases having improved properties and method for improved isothermal amplification of a target DNA. US Patent 11,371,028 (2021).

  • Plaper, T. et al. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci. Rep. 11, 9136 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lainšček, D. et al. Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing. Nat. Commun. 13, 3604 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, B. et al. Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01947-w (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trojan, J. et al. Functional analysis of hMLH1 variants and HNPCC-related mutations using a human expression system. Gastroenterology 122, 211–219 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Roberts, T. C., Langer, R. & Wood, M. J. A. Advances in oligonucleotide drug delivery. Nat. Rev. Drug Discov. 19, 673–694 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pan, W. et al. DNA polymerase preference determines PCR priming efficiency. BMC Biotech. 14, 10 (2014).

    Article 

    Google Scholar
     

  • Choi, J. et al. Precise genomic deletions using paired prime editing. Nat. Biotechnol. 40, 218–226 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jiang, T., Zhang, X. O., Weng, Z. & Xue, W. Deletion and replacement of long genomic sequences using prime editing. Nat. Biotechnol. 40, 227–234 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zheng, C. et al. Template-jumping prime editing enables large insertion and exon rewriting in vivo. Nat. Commun. 14, 3369 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, J. et al. Efficient targeted insertion of large DNA fragments without DNA donors. Nat. Methods 19, 331–340 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gasiunas, G. et al. A catalogue of biochemically diverse CRISPR–Cas9 orthologs. Nat. Commun. 11, 5512 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374, 57–65 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martín-Alonso, S., Frutos-Beltrán, E. & Menéndez-Arias, L. Reverse transcriptase: from transcriptomics to genome editing. Trends Biotechnol. 39, 194–210 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Shuto, Y. et al. Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature 631, 224–231 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, L. et al. Efficient delivery of antisense oligonucleotides using bioreducible lipid nanoparticles in vitro and in vivo. Mol. Ther. Nucleic Acids 19, 1357–1367 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Farbiak, L. et al. All‐in‐one dendrimer‐based lipid nanoparticles enable precise HDR‐mediated gene editing in vivo. Adv. Mater. 33, 2006619 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Dahlman, J. E. et al. Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics. Proc. Natl Acad. Sci. USA 114, 2060–2065 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xue, L. et al. High-throughput barcoding of nanoparticles identifies cationic, degradable lipid-like materials for mRNA delivery to the lungs in female preclinical models. Nat. Commun. 15, 1884 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, K. et al. Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR–Cas9 RNP. Preprint at https://doi.org/10.1101/2023.11.15.566339 (2023).

  • Wei, T. et al. Lung SORT LNPs enable precise homology-directed repair mediated CRISPR/Cas genome correction in cystic fibrosis models. Nat. Commun. 14, 7322 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Onuma, H., Sato, Y. & Harashima, H. Lipid nanoparticle-based ribonucleoprotein delivery for in vivo genome editing. J. Controlled Release 355, 406–416 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Kazlauskas, D., Varsani, A., Koonin, E. V. & Krupovic, M. Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. Nat. Commun. 10, 3425 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleinstiver, B. P. et al. Engineered CRISPR–Cas9 nucleases with altered PAM specificities. Nature 523, 481–485 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939–946 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleinstiver, B. P. et al. Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat. Biotechnol. 37, 276–282 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • BBMap. SourceForge https://sourceforge.net/projects/bbmap (2022).

  • Iseli, C., Ambrosini, G., Bucher, P. & Jongeneel, C. V. Indexing strategies for rapid searches of short words in genome sequences. PLoS One 2, e579 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ferreira da Silva J., et al. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. (Dataset. NCBI Sequence Read Archive); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1015647 (2024).



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