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

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

Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature578, 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. Cell63, 633–646 (2016).

Article 
PubMed 

Google Scholar 

Shen, M. W. et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature563, 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. USA118, 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. Nature533, 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. Nature551, 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. Nature569, 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. Science364, 289–292 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Park, S. & Beal, P. A. Off-target editing by CRISPR-guided DNA base editors. Biochemistry58, 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 Discovery19, 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. Nature560, 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. Cell175, 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. Nature576, 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 Cell12, 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. USA115, 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. mBio14, 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. eLife12, 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. Cell184, 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. Science245, 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. Nature533, 125–129 (2016).

Article 
CAS 
PubMed 

Google Scholar 

Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell186, 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. Methods20, 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. Bioinformatics30, 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. Cell16, 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. USA102, 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. USA107, 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. Gastroenterology122, 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. Methods19, 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. Science374, 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. Nature631, 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 Acids19, 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. USA114, 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 Release355, 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. Nature523, 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 One2, 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).

>>> Read full article>>>
Copyright for syndicated content belongs to the linked Source : Nature.com – https://www.nature.com/articles/s41587-024-02324-x

Exit mobile version