Bestdealss

Better Easy Saving Troops

Retargeted serine integrases for one-step, exact integration of enormous DNA sequences in human cells – Nature Biotechnology

Retargeted serine integrases for one-step, exact integration of enormous DNA sequences in human cells – Nature Biotechnology


  • Urnov, F. D. et al. Extremely environment friendly endogenous human gene correction utilizing designed zinc-finger nucleases. Nature 435, 646–651 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Perez, C. et al. Components affecting double-strand break-induced homologous recombination in mammalian cells. Biotechniques 39, 109–115 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kosicki, M., Tomberg, Ok. & Bradley, A. Restore of double-strand breaks induced by CRISPR–Cas9 results in giant deletions and complicated rearrangements. Nat. Biotechnol. 36, 765–771 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

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

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pabo, C. O., Peisach, E. & Grant, R. A. Design and choice of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 70, 313–340 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ichikawa, D. M. et al. A common deep-learning mannequin for zinc finger design allows transcription issue reprogramming. Nat. Biotechnol. 41, 1117–1129 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Carroll, D. Genome engineering with zinc-finger nucleases. Genetics 188, 773–782 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–1512 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Miller, J. C. et al. A TALE nuclease structure for environment friendly genome modifying. Nat. Biotechnol. 29, 143–148 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Akopian, A., He, J., Boocock, M. R. & Stark, W. M. Chimeric recombinases with designed DNA sequence recognition. Proc. Natl Acad. Sci. USA 100, 8688–8691 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chaikind, B., Bessen, J. L., Thompson, D. B., Hu, J. H. & Liu, D. R. A programmable Cas9–serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucleic Acids Res. 44, 9758–9770 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gaj, T., Mercer, A. C., Sirk, S. J., Smith, H. L. & Barbas, C. F. third A complete method to zinc-finger recombinase customization allows genomic focusing on in human cells. Nucleic Acids Res. 41, 3937–3946 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gordley, R. M., Gersbach, C. A. & Barbas, C. F. third Synthesis of programmable integrases. Proc. Natl Acad. Sci. USA 106, 5053–5058 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mercer, A. C., Gaj, T., Fuller, R. P. & Barbas, C. F. third Chimeric TALE recombinases with programmable DNA sequence specificity. Nucleic Acids Res. 40, 11163–11172 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Prorocic, M. M. et al. Zinc-finger recombinase actions in vitro. Nucleic Acids Res. 39, 9316–9328 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Standage-Beier, Ok. et al. RNA-guided recombinase–Cas9 fusion targets genomic DNA deletion and integration. CRISPR J. 2, 209–222 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Voziyanova, E., Li, F., Shah, R. & Voziyanov, Y. Genome focusing on by hybrid Flp–TAL recombinases. Sci. Rep. 10, 17479 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mukhametzyanova, L. et al. Activation of recombinases at particular DNA loci by zinc-finger area insertions. Nat. Biotechnol. 42, 1844–1854 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Feng, X., Bednarz, A. L. & Colloms, S. D. Exact focused integration by a chimaeric transposase zinc-finger fusion protein. Nucleic Acids Res. 38, 1204–1216 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Owens, J. B. et al. Transcription activator like effector (TALE)-directed piggyBac transposition in human cells. Nucleic Acids Res. 41, 9197–9207 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Owens, J. B. et al. Chimeric piggyBac transposases for genomic focusing on in human cells. Nucleic Acids Res. 40, 6978–6991 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ye, L. et al. TAL effectors mediate high-efficiency transposition of the piggyBac transposon in silkworm Bombyx mori L. Sci. Rep. 5, 17172 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yant, S. R., Huang, Y., Akache, B. & Kay, M. A. Web site-directed transposon integration in human cells. Nucleic Acids Res. 35, e50 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Klompe, S. E., Vo, P. L. H., Halpin-Healy, T. S. & Sternberg, S. H. Transposon-encoded CRISPR–Cas methods direct RNA-guided DNA integration. Nature 571, 219–225 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Strecker, J. et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science 365, 48–53 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lampe, G. D. et al. Focused DNA integration in human cells with out double-strand breaks utilizing CRISPR-associated transposases. Nat. Biotechnol. 42, 87–98 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Witte, I. P. et al. Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase. Science 388, eadt5199 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Durrant, M. G. et al. Bridge RNAs direct programmable recombination of goal and donor DNA. Nature 630, 984–993 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Merrick, C. A., Zhao, J. & Rosser, S. J. Serine integrases: advancing artificial biology. ACS Synth. Biol. 7, 299–310 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Bessen, J. L. et al. Excessive-resolution specificity profiling and off-target prediction for site-specific DNA recombinases. Nat. Commun. 10, 1937 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Campbell, A. M. Chromosomal insertion websites for phages and plasmids. J. Bacteriol. 174, 7495–7499 (1992).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kim, A. I. et al. Mycobacteriophage Bxb1 integrates into the Mycobacterium smegmatis groEL1 gene. Mol. Microbiol. 50, 463–473 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ghosh, P., Kim, A. I. & Hatfull, G. F. The orientation of mycobacteriophage Bxb1 integration is solely depending on the central dinucleotide of attP and attB. Mol. Cell 12, 1101–1111 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ghosh, P., Wasil, L. R. & Hatfull, G. F. Management of phage Bxb1 excision by a novel recombination directionality issue. PLoS Biol. 4, e186 (2006).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Anzalone, A. V. et al. Programmable deletion, alternative, integration and inversion of enormous DNA sequences with twin prime modifying. Nat. Biotechnol. 40, 731–740 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Yarnall, M. T. N. et al. Drag-and-drop genome insertion of enormous sequences with out double-strand DNA cleavage utilizing CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pandey, S. et al. Environment friendly site-specific integration of enormous genes in mammalian cells through constantly developed recombinases and prime modifying. Nat. Biomed. Eng. 9, 22–39 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, P. et al. Rising intracellular dNTP ranges improves prime modifying effectivity. Nat. Biotechnol. 43, 539–544 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Xu, Z. et al. Accuracy and effectivity outline Bxb1 integrase as the most effective of fifteen candidate serine recombinases for the combination of DNA into the human genome. BMC Biotechnol. 13, 87 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rebar, E. J. & Pabo, C. O. Zinc finger phage: affinity choice of fingers with new DNA-binding specificities. Science 263, 671–673 (1994).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Greisman, H. A. & Pabo, C. O. A normal technique for choosing high-affinity zinc finger proteins for numerous DNA goal websites. Science 275, 657–661 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Karpinski, J. et al. Directed evolution of a recombinase that excises the provirus of most HIV-1 main isolates with excessive specificity. Nat. Biotechnol. 34, 401–409 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lansing, F. et al. Correction of an element VIII genomic inversion with designer-recombinases. Nat. Commun. 13, 422 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rutherford, Ok., Yuan, P., Perry, Ok., Sharp, R. & van Duyne, G. D. Attachment web site recognition and regulation of directionality by the serine integrases. Nucleic Acids Res. 41, 8341–8356 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H., Sharp, R., Rutherford, Ok., Gupta, Ok. & van Duyne, G. D. Serine integrase attP binding and specificity. J. Mol. Biol. 430, 4401–4418 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Baek, M. et al. Correct prediction of protein constructions and interactions utilizing a three-track neural community. Science 373, 871–876 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gersbach, C. A., Gaj, T., Gordley, R. M. & Barbas, C. F. third Directed evolution of recombinase specificity by break up gene reassembly. Nucleic Acids Res. 38, 4198–4206 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pavletich, N. P. & Pabo, C. O. Zinc finger–DNA recognition: crystal construction of a Zif268–DNA advanced at 2.1 A. Science 252, 809–817 (1991).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zheng, Z. et al. Anchored multiplex PCR for focused next-generation sequencing. Nat. Med. 20, 1479–1484 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

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

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Arellano-Carbajal, F. et al. Macoilin, a conserved nervous system-specific ER membrane protein that regulates neuronal excitability. PLoS Genet. 7, e1001341 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McCorvie, T. J. et al. Molecular foundation for the regulation of human glycogen synthase by phosphorylation and glucose-6-phosphate. Nat. Struct. Mol. Biol. 29, 628–638 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kotin, R. M., Linden, R. M. & Berns, Ok. I. Characterization of a most well-liked web site on human chromosome 19q for integration of adeno-associated virus DNA by non-homologous recombination. EMBO J. 11, 5071–5078 (1992).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Peng, J. et al. Dusty protein kinases: main construction, gene evolution, tissue particular expression and distinctive options of the catalytic area. Biochim. Biophys. Acta 1759, 562–572 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Roth, T. L. et al. Reprogramming human T cell perform and specificity with non-viral genome focusing on. Nature 559, 405–409 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hornung, V. & Latz, E. Intracellular DNA recognition. Nat. Rev. Immunol. 10, 123–130 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Inniss, M. C. et al. A novel Bxb1 integrase RMCE system for prime constancy site-specific integration of mAb expression cassette in CHO cells. Biotechnol. Bioeng. 114, 1837–1846 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, X. et al. Bxb1 integrase serves as a extremely environment friendly DNA recombinase in fast metabolite pathway meeting. Acta Biochim. Biophys. Sin. (Shanghai) 49, 44–50 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Thomson, J. G. et al. The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis. BMC Biotechnol. 12, 9 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Blechl, A., Lin, J., Shao, M., Thilmony, R. & Thomson, J. The Bxb1 recombinase mediates site-specific deletion in transgenic wheat. Plant Mol. Biol. Report. 30, 1357–1366 (2012).

    Article 
    CAS 

    Google Scholar 

  • Jiang, L. et al. Goal strains for recombinase-mediated gene stacking in soybean. Theor. Appl. Genet. 135, 1163–1175 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Durrant, M. G. et al. Systematic discovery of recombinases for environment friendly integration of enormous DNA sequences into the human genome. Nat. Biotechnol. 41, 488–499 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • McCarty, D. M. et al. Adeno-associated virus terminal repeat (TR) mutant generates self-complementary vectors to beat the rate-limiting step to transduction in vivo. Gene Ther. 10, 2112–2118 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhang, C. P. et al. Environment friendly non-viral supply of macromolecules in human main hematopoietic stem cells and lymphocytes. J. Mol. Cell Biol. 15, mjad018 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Migliori, V. et al. ONE-STEP tagging: a flexible methodology for fast site-specific integration by simultaneous reagent supply. Nucleic Acids Res. 53, gkaf809 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tareen, A. & Kinney, J. B. Logomaker: lovely sequence logos in Python. Bioinformatics 36, 2272–2274 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Passaro, S. et al. Boltz-2: in direction of correct and environment friendly binding affinity prediction. Preprint at bioRxiv (2025).

  • Bakalar, M. H. et al. Giant serine integrase off-target discovery with deep studying for genome broad prediction. Preprint at bioRxiv (2024).

  • Leave a Reply

    Your email address will not be published. Required fields are marked *