Recent technology advancements in large-scale DNA assembly

References

[1] Venter JC , Glass JI , Hutchison CA , Vashee S . Synthetic chromosomes, genomes, viruses, and cells. Cell. 2022; 185 (15): 2708- 24.

[2] Blount BA , Lu X , Driessen MRM , Jovicevic D , Sanchez MI , Ciurkot K , et al. Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics. Cell Genom. 2023; 3 (11): 100418.

[3] Foo JL , Kitano S , Susanto AV , Jin Z , Lin Y , Luo Z , et al. Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration. Cell Genom. 2023; 3 (11): 100435.

[4] Lauer S , Luo J , Lazar-Stefanita L , Zhang W , McCulloch LH , Fanfani V , et al. Context-dependent neocentromere activity in synthetic yeast chromosome VⅢ. Cell Genom. 2023; 3 (11): 100437.

[5] Luo J , Vale-Silva LA , Raghavan AR , Mercy G , Heldrich J , Sun X , et al. Synthetic chromosome fusion: effects on mitotic and meiotic genome structure and function. Cell Genom. 2023; 3 (11): 100439.

[6] McCulloch LH , Sambasivam V , Hughes AL , Annaluru N , Ramalingam S , Fanfani V , et al. Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains. Cell Genom. 2023; 3 (11): 100419.

[7] Schindler D , Walker RSK , Jiang S , Brooks AN , Wang Y , Müller CA , et al. Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell. 2023; 186 (24): 5237- 53.e22.

[8] Shen Y , Gao F , Wang Y , Wang Y , Zheng J , Gong J , et al. Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VⅡ and SCRaMbLEing synthetic disomic yeast. Cell Genom. 2023; 3 (11): 100364.

[9] Williams TC , Kroukamp H , Xu X , Wightman ELI , Llorente B , Borneman AR , et al. Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. Cell Genom. 2023; 3 (11): 100379.

[10] Zhang W , Lazar-Stefanita L , Yamashita H , Shen MJ , Mitchell LA , Kurasawa H , et al. Manipulating the 3D organization of the largest synthetic yeast chromosome. Mol Cell. 2023; 83 (23): 4424- 37.e5.

[11] Zhao Y , Coelho C , Hughes AL , Lazar-Stefanita L , Yang S , Brooks AN , et al. Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions. Cell. 2023; 186 (24): 5220- 36.e16.

[12] Chen LG , Lan T , Zhang S , Zhao M , Luo G , Gao Y , et al. A designer synthetic chromosome fragment functions in moss. Nat Plants. 2024; 26 (2): 1- 12.

[13] Hoose A , Vellacott R , Storch M , Freemont PS , Ryadnov MG . DNA synthesis technologies to close the gene writing gap. Nat Rev Chem. 2023; 7 (3): 144- 61.

[14] Casini A , Storch M , Baldwin GS , Ellis T . Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol. 2015; 16 (9): 568- 76.

[15] Chao R , Yuan Y , Zhao H . Recent advances in DNA assembly technologies. FEMS Yeast Res. 2015; 15 (1): 1- 9.

[16] Ellis T , Adie T , Baldwin GS . DNA assembly for synthetic biology: from parts to pathways and beyond. Integr Biol. 2011; 3 (2): 109- 18.

[17] Shetty RP , Endy D , Knight TF . Engineering BioBrick vectors from BioBrick parts. J Biol Eng. 2008; 2 (1): 5.

[18] Agmon N , Mitchell LA , Cai Y , Ikushima S , Chuang J , Zheng A , et al. Yeast Golden Gate (yGG) for the efficient assembly of S. cerevisiae transcription units. ACS Synth Biol. 2015; 4 (7): 853- 9.

[19] Guo Y , Dong J , Zhou T , Auxillos J , Li T , Zhang W , et al. YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae. Nucleic Acids Res. 2015; 43 (13): e88.

[20] Gibson DG , Young L , Chuang RY , Venter JC , Hutchison CA , Smith HO . Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009; 6 (5): 343- 5.

[21] Stemmer WPC , Crameri A , Ha KD , Brennan TM , Heyneker HL . Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. 1995; 164 (1): 49- 53.

[22] Gibson DG , Benders GA , Andrews-Pfannkoch C , Denisova EA , Baden-Tillson H , Zaveri J , et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008; 319 (5867): 1215- 20.

[23] Adams BL . The next generation of synthetic biology chassis: moving synthetic biology from the laboratory to the field. ACS Synth Biol. 2016; 5 (12): 1328- 30.

[24] O’Connor M , Peifer M , Bender W . Construction of large DNA segments in Escherichia coli. Science. 1989; 244 (4910): 1307- 12.

[25] Zhang Y , Buchholz F , Muyrers JPP , Stewart AF . A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet. 1998; 20 (2): 123- 8.

[26] Fu J , Bian X , Hu S , Wang H , Huang F , Seibert PM , et al. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol. 2012; 30 (5): 440- 6.

[27] Wannier TM , Ciaccia PN , Ellington AD , Filsinger GT , Isaacs FJ , Javanmardi K , et al. Recombineering and MAGE. Nat Rev Methods Primers. 2021; 1 (1): 1- 24.

[28] Robertson WE , Funke LFH , de la Torre D , Fredens J , Wang K , Chin JW . Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS. Nat Protoc. 2021; 16 (5): 2345- 80.

[29] Fredens J , Wang K , de la Torre D , Funke LFH , Robertson WE , Christova Y , et al. Total synthesis of Escherichia coli with a recoded genome. Nature. 2019; 569 (7757): 514- 8.

[30] Zürcher JF , Kleefeldt AA , Funke LFH , Birnbaum J , Fredens J , Grazioli S , et al. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature. 2023; 619 (7970): 555- 62.

[31] Juhas M , Ajioka JW . Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome. J Microbiol Methods. 2016; 125: 1- 7.

[32] Itaya M . Toward a bacterial genome technology: integration of the Escherichia coli prophage lambda genome into the Bacillus subtilis 168 chromosome. Mol Gen Genet. 1995; 248 (1): 9- 16.

[33] Itaya M , Tsuge K , Koizumi M , Fujita K . Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci USA. 2005; 102 (44): 15971- 6.

[34] Itaya M , Fujita K , Kuroki A , Tsuge K . Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat Methods. 2008; 5 (1): 41- 3.

[35] Ogawa T , Iwata T , Kaneko S , Itaya M , Hirota J . An inducible recA expression Bacillus subtilis genome vector for stable manipulation of large DNA fragments. BMC Genom. 2015; 16 (1): 209.

[36] Shao Y , Lu N , Cai C , Zhou F , Wang S , Zhao Z , et al. A single circular chromosome yeast. Cell Res. 2019; 29 (1): 87- 9.

[37] Gibson DG . Gene and genome construction in yeast. Curr Protoc Mol Biol. 2011; 94 (1): 3.22.1- 3.22.17.

[38] Kouprina N , Larionov V . TAR cloning: insights into gene function, long-range haplotypes and genome structure and evolution. Nat Rev Genet. 2006; 7 (10): 805- 12.

[39] Larionov V , Kouprina N , Solomon G , Barrett JC , Resnick MA . Direct isolation of human BRCA2 gene by transformation-associated recombination in yeast. Proc Natl Acad Sci USA. 1997; 94 (14): 7384- 7.

[40] Jiang S , Tang Y , Xiang L , Zhu X , Cai Z , Li L , et al. Efficient de novo assembly and modification of large DNA fragments. Sci China Life Sci. 2022; 65 (7): 1445- 55.

[41] Mitchell LA , Chuang J , Agmon N , Khunsriraksakul C , Phillips NA , Cai Y , et al. Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res. 2015; 43 (13): 6620- 30.

[42] Kuijpers NG , Chroumpi S , Vos T , Solis-Escalante D , Bosman L , Pronk JT , et al. One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. FEMS Yeast Res. 2013; 13 (8): 769- 81.

[43] Zhou J , Wu R , Xue X , Qin Z . CasHRA (Cas9-facilitated homologous recombination assembly) method of constructing megabase-sized DNA. Nucleic Acids Res. 2016; 44 (14): e124.

[44] Richardson SM , Mitchell LA , Stracquadanio G , Yang K , Dymond JS , DiCarlo JE , et al. Design of a synthetic yeast genome. Science. 2017; 355 (6329): 1040- 4.

[45] Mitchell LA , McCulloch LH , Pinglay S , Berger H , Bosco N , Brosh R , et al. De novo assembly and delivery to mouse cells of a 101 kb functional human gene. Genetics. 2021; 218 (1): iyab038.

[46] Zhang W , Zhao G , Luo Z , Lin Y , Wang L , Guo Y , et al. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science. 2017; 355 (6329): eaaf3981.

[47] Shen Y , Wang Y , Chen T , Gao F , Gong J , Abramczyk D , et al. Deep functional analysis of synⅡ, a 770-kilobase synthetic yeast chromosome. Science. 2017; 355 (6329): eaaf4791.

[48] Xie ZX , Li BZ , Mitchell LA , Wu Y , Qi X , Jin Z , et al. “Perfect” designer chromosome V and behavior of a ring derivative. Science. 2017; 355 (6329): eaaf4704.

[49] He B , Ma Y , Tian F , Zhao GR , Wu Y , Yuan YJ . YLC-assembly: large DNA assembly via yeast life cycle. Nucleic Acids Res. 2023; 51 (15): 8283- 92.

[50] Ma Y , Su S , Fu Z , Zhou C , Qiao B , Wu Y , et al. Convenient synthesis and delivery of a megabase-scale designer accessory chromosome empower biosynthetic capacity. Cell Res. 2024; 8 (4): 1- 14.

[51] Coradini ALV , Ville CN , Krieger ZA , Roemer J , Hull C , Yang S , et al. Building synthetic chromosomes from natural DNA. Nat Commun. 2023; 14 (1): 8337.

[52] Boeke JD , Church G , Hessel A , Kelley NJ , Arkin A , Cai Y , et al. The genome project-write. Science. 2016; 353 (6295): 126- 7.

[53] Zhang XE , Liu C , Dai J , Yuan Y , Gao C , Feng Y , et al. Enabling technology and core theory of synthetic biology. Sci China Life Sci. 2023; 6 (8): 1- 44.

[54] Ohtani N , Hasegawa M , Sato M , Tomita M , Kaneko S , Itaya M . Serial assembly of Thermus megaplasmid DNA in the genome of Bacillus subtilis 168: a BAC-based domino method applied to DNA with a high GC content. Biotechnol J. 2012; 7 (7): 867- 76.

[55] Jiang W , Zhao X , Gabrieli T , Lou C , Ebenstein Y , Zhu TF . Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nat Commun. 2015; 6 (1): 8101.

[56] Enghiad B , Huang C , Guo F , Jiang G , Wang B , Tabatabaei SK , et al. Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination. Nat Commun. 2021; 12 (1): 1171.

[57] Zhang W , Golynker I , Brosh R , Fajardo A , Zhu Y , Wudzinska AM , et al. Mouse genome rewriting and tailoring of three important disease loci. Nature. 2023; 623 (7986): 423- 31.

[58] Li R , Li Z , Ma K , Wang G , Li W , Liu H , et al. Strategy for efficient cloning of biosynthetic gene clusters from fungi. Sci China Life Sci. 2019; 62: 1087- 95.

[59] Bailey-Serres J , Parker JE , Ainsworth EA , Oldroyd GED , Schroeder JI . Genetic strategies for improving crop yields. Nature. 2019; 575 (7781): 109- 18.

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