Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).
Gibson, D. G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 (2008).
Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010).
Wang, K. H. et al. Defining synonymous codon compression schemes by genome recoding. Nature 539, 59–64 (2016).
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Kouprina, N. & Larionov, V. TAR cloning: insights into gene function, long-range haplotypes and genome structure and evolution. Nat. Rev. Genet. 7, 805–812 (2006).
Wang, K., de la Torre, D., Robertson, W. E. & Chin, J. W. Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly. Science 365, 922–926 (2019).
Ma, N. J., Moonan, D. W. & Isaacs, F. J. Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering. Nat. Protoc. 9, 2285–2300 (2014).
Robertson, W. E. et al. Sense codon reassignment enables viral resistance and encoded polymer synthesis. Science 372, 1057–1062 (2021).
Zurcher, J. F. et al. Refactored genetic codes enable bidirectional genetic isolation. Science 378, 516–523 (2022).
Nyerges, A. et al. A swapped genetic code prevents viral infections and gene transfer. Nature 615, 720–727 (2023).
Spinck, M. et al. Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles. Nat. Chem. 15, 61–69 (2023).
Richardson, S. M. et al. Design of a synthetic yeast genome. Science 355, 1040–1044 (2017).
Lajoie, M. J. et al. Genomically recoded organisms expand biological functions. Science 342, 357–360 (2013).
Ostrov, N. et al. Design, synthesis, and testing toward a 57-codon genome. Science 353, 819–822 (2016).
Lau, Y. H. et al. Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA. Nucleic Acids Res. 45, 6971–6980 (2017).
Hutchison, C. A. 3rd et al. Design and synthesis of a minimal bacterial genome. Science 351, aad6253 (2016).
Shao, Y. et al. Creating a functional single-chromosome yeast. Nature 560, 331–335 (2018).
Giani, A. M., Gallo, G. R., Gianfranceschi, L. & Formenti, G. Long walk to genomics: history and current approaches to genome sequencing and assembly. Comput. Struct. Biotechnol. J. 18, 9–19 (2020).
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Neil, D. L. et al. Structural instability of human tandemly repeated DNA sequences cloned in yeast artificial chromosome vectors. Nucleic Acids Res. 18, 1421–1428 (1990).
Haubold, B. & Wiehe, T. How repetitive are genomes? BMC Bioinform. https://doi.org/10.1186/1471-2105-7-541 (2006).
Yoneji, T., Fujita, H., Mukai, T. & Su’etsugu, M. Grand scale genome manipulation via chromosome swapping in Escherichia coli programmed by three one megabase chromosomes. Nucleic Acids Res. 49, 8407–8418 (2021).
Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA 97, 5978–5983 (2000).
Mejia, J. E. & Larin, Z. The assembly of large BACs by in vivo recombination. Genomics 70, 165–170 (2000).
Mukai, T. et al. Overcoming the challenges of megabase-sized plasmid construction in Escherichia coli. ACS Synth. Biol. 9, 1315–1327 (2020).
Kotzamanis, G. & Huxley, C. Recombining overlapping BACs into a single larger BAC. BMC Biotechnol. 4, 1 (2004).
Sopher, B. L. & La Spada, A. R. Efficient recombination-based methods for bacterial artificial chromosome fusion and mutagenesis. Gene 371, 136–143 (2006).
Lovett, S. T. in Bacterial Stress Responses 2nd edn (eds Storz, G. & Hengge, R.) 205–228 (2011); https://doi.org/10.1128/9781555816841.ch13.
Anstey-Gilbert, C. S. et al. The structure of Escherichia coli ExoIX-implications for DNA binding and catalysis in flap endonucleases. Nucleic Acids Res. 41, 8357–8367 (2013).
Liu, Y., Kao, H. I. & Bambara, R. A. Flap endonuclease 1: a central component of DNA metabolism. Annu. Rev. Biochem. 73, 589–615 (2004).
Ellsworth, R. E. et al. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc. Natl Acad. Sci. USA 97, 1172–1177 (2000).
Krzywinski, M. et al. A set of BAC clones spanning the human genome. Nucleic Acids Res. 32, 3651–3660 (2004).
Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
Sun, J. X. et al. A direct characterization of human mutation based on microsatellites. Nat. Genet. 44, 1161–1165 (2012).
Szklarczyk, D. et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49, 10800–10800 (2021).
van der Oost, J. & Patinios, C. The genome editing revolution. Trends Biotechnol. 41, 396–409 (2023).
Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233–239 (2013).
Tong, Y., Jorgensen, T. S., Whitford, C. M., Weber, T. & Lee, S. Y. A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing. Nat. Commun. 12, 5206 (2021).
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Waters, V. L. Conjugation between bacterial and mammalian cells. Nat. Genet. 29, 375–376 (2001).
Lee, E. C. et al. Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery. Nat. Biotechnol. 32, 356–363 (2014).
Macdonald, L. E. et al. Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes. Proc. Natl Acad. Sci. USA 111, 5147–5152 (2014).
Pansegrau, W. et al. Complete nucleotide-sequence of Birmingham IncPα plasmids—compilation and comparative-analysis. J. Mol. Biol. 239, 623–663 (1994).
Robertson, W. E. et al. Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS. Nat. Protoc. https://doi.org/10.1038/s41596-020-00464-3 (2021).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://doi.org/10.48550/arXiv.1303.3997 (2013).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience https://doi.org/10.1093/gigascience/giab008 (2021).
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Smolka, M. et al. Comprehensive structural variant detection: from mosaic to population-level. Preprint at bioRxiv https://doi.org/10.1101/2022.04.04.487055 (2022).
Cer, R. Z. et al. Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. Nucleic Acids Res. 41, D94–D100 (2013).
Schubert, M. G. et al. High-throughput functional variant screens via in vivo production of single-stranded DNA. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.2018181118 (2021).
- SEO Powered Content & PR Distribution. Get Amplified Today.
- PlatoData.Network Vertical Generative Ai. Empower Yourself. Access Here.
- PlatoAiStream. Web3 Intelligence. Knowledge Amplified. Access Here.
- PlatoESG. Automotive / EVs, Carbon, CleanTech, Energy, Environment, Solar, Waste Management. Access Here.
- BlockOffsets. Modernizing Environmental Offset Ownership. Access Here.
- Source: https://www.nature.com/articles/s41586-023-06268-1