synthetic biology; synthetic genomics; DNA synthesis; genome assembly; genome transplant
As an interdisciplinary subject between biology and engineering, synthetic biology has shown more and more applications in the fields of biomedicine, energy, new material, etc. Synthetic genomics focusing on de novo design and synthesis of new life system is one of the major directions in synthetic biology which relies on serial techniques including DNA synthesis, assembly, transplantation, etc. Here, we summary the current developments on technologies in genome synthesis, which aims to deepen the comprehension of the technique systems and shed light to the future development in this field.
Bulletin of Chinese Academy of Sciences
Michelson A M, Todd A R. Nucleotides part ⅩⅩⅩⅡ. Synthesis of a dithymidine dinucleotide containing a 3'-5'-internucleotidic linkage. J Chem Soc, 1955:2632-2638.
Beaucage S L, Caruthers M H. Deoxynucleoside phosphoramidites-a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett, 1981, 22(20):1859-1862.
Kosuri S, Church G M. Large-scale de novo DNA synthesis:technologies and applications. Nat Methods, 2014, 11(5):499-507.
Kosuri S, Eroshenko N, Leproust E M, et al. Scalable gene synthesis by selective amplification of DNA pools from highfidelity microchips. Nat Biotechnol, 2010, 28(12):1295-1299.
Matzas M, Stahler P F, Kefer N, et al. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using highthroughput pyrosequencing. Nat Biotechnol, 2010, 28(12):1291-1294.
Algire M, Krishnakumar R, Merryman C. Megabases for kilodollars. Nat Biotechnol, 2010, 28(12):1272-1273.
Palluk S, Arlow D H, de Rond T, et al. De novo DNA synthesis using polymerase-nucleotide conjugates. Nat Biotechnol, 2018, 36(7):645-650.
Bollum F J. Oligodeoxyribonucleotide-primed reactions catalyzed by calf thymus polymerase. J Biol Chem, 1962, 237(6):1945-1949.
Jensen M A, Davis R W. Template-independent enzymatic oligonucleotide synthesis (TiEOS):Its history, prospects, and challenges. Biochemistry, 2018, 57(12):1821-1832.
Stemmer W P, Crameri A, Ha K D, et al. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene, 1995, 164(1):49-53.
Smith H O, Hutchison C A, Pfannkoch C, et al. Generating a synthetic genome by whole genome assembly:phi X174 bacteriophage from synthetic oligonucleotides. PNAS, 2003, 100(26):15440-15445.
Shetty R P, Endy D, Knight T F Jr. Engineering BioBrick vectors from BioBrick parts. J Biol Eng, 2008, 2:5.
Anderson J C, Dueber J E, Leguia M, et al. BglBricks:A flexible standard for biological part assembly. J Biol Eng, 2010, 4(1):1.
Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One, 2008, 3(11):e3647.
Guo Y, Dong J, Zhou T, et al. YeastFab:the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae. Nucleic Acids Res, 2015, 43(13):e88.
Qin Y, Tan C, Lin J, et al. Ecoexpress-highly efficient construction and expression of multicomponent protein complexes in Escherichia coli. ACS Synth Biol, 2016, 5(11):1239-1246.
Gibson D G, Young L, Chuang R Y, et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods, 2009, 6(5):343.
Liu J K, Chen W H, Ren S X, et al. iBrick:A new standard for iterative assembly of biological parts with homing endonucleases. PLoS One, 2014, 9(10):e110852.
Li S Y, Zhao G P, Wang J. C-Brick:A new standard for assembly of biological parts using Cpf1. ACS Synth Biol, 2016, 5(12):1383-1388.
Weber E, Engler C, Gruetzner R, et al. A modular cloning system for standardized assembly of multigene constructs. PLoS One, 2011, 6(2):e16765.
Sarrion-Perdigones A, Vazquez-Vilar M, Palaci J, et al. GoldenBraid 2.0:A comprehensive DNA assembly framework for plant synthetic biology. Plant Physiol, 2013, 162(3):1618-1631.
Chen W H, Qin Z J, Wang J, et al. The MASTER (methylationassisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Res, 2013, 41(8):e93.
Li M V, Shukla D, Rhodes B H, et al. HomeRun Vector Assembly System:a flexible and standardized cloning system for assembly of multi-modular DNA constructs. PLoS One, 2014, 9(6):e100948.
Lampropoulos A, Sutikovic Z, Wenzl C, et al. GreenGate-a novel, versatile, and efficient cloning system for plant transgenesis. PLoS One, 2013, 8(12):e83043.
Wang X, Sa N, Tian P F, et al. Classifying DNA assembly protocols for devising cellular architectures. Biotechnol Adv, 2011, 29(1):156-163.
Hinnen A, Hicks J B, Fink G R. Transformation of yeast. PNAS, 1978, 75(4):1929-1933.
Orr-Weaver T L, Szostak J W, Rothstein R J. Yeast transformation:a model system for the study of recombination. PNAS, 1981, 78(10):6354-6358.
Gibson D G, Benders G A, Axelrod K C, et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. PNAS, 2008, 105(51):20404-20409.
Silverman G A, Jockel J I, Domer P H, et al. Yeast artificial chromosome cloning of a two-megabase-size contig within chromosomal band 18q21 establishes physical linkage between BCL2 and plasminogen activator inhibitor type-2. Genomics, 1991, 9(2):219-228.
Gibson D G, Glass J I, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 2010, 329(5987):52-56.
Dymond J S, Richardson S M, Coombes C E, et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011, 477(7365):471-476.
Annaluru N, Muller H, Mitchell L A, et al. Total synthesis of a functional designer eukaryotic chromosome. Science, 2014, 344(6179):55-58.
Shen Y, Wang Y, Chen T, et al. Deep functional analysis of synⅡ, a 770-kilobase synthetic yeast chromosome. Science, 2017, 355(6329), doi:10.1126/science.aaf4791.
Xie Z X, Li B Z, Mitchell L A, et al. "Perfect" designer chromosome V and behavior of a ring derivative. Science, 2017, 355(6329), doi:10.1126/science.aaf4704.
Mitchell L A, Wang A, Stracquadanio G, et al. Synthesis, debugging, and effects of synthetic chromosome consolidation:synⅥ and beyond. Science, 2017, 355(6329), doi:10.1126/science.aaf4831.
Wu Y, Li B Z, Zhao M, et al. Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 2017, 355(6329), doi:10.1126/science.aaf4706.
Zhang W M, Zhao G H, Luo Z Q, et al. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science, 2017, 355(6329), doi:10.1126/science.aaf3981.
Shao Y, Lu N, Wu Z, et al. Creating a functional singlechromosome yeast. Nature, 2018, 560(7718):331-335.
Boeke J D, Church G, Hessel A, et al. The Genome Project-Write. Science, 2016, 353(6295):126-127.
de Jong G, Telenius A, Vanderbyl S, et al. Efficient in-vitro transfer of a 60-Mb mammalian artificial chromosome into murine and hamster cells using cationic lipids and dendrimers. Chromosome Res, 2001, 9(6):475-485.
Co D O, Borowski A H, Leung J D, et al. Generation of transgenic mice and germline transmission of a mammalian artificial chromosome introduced into embryos by pronuclear microinjection. Chromosome Res, 2000, 8(3):183-191.
Telenius H, Szeles A, Kereso J, et al. Stability of a functional murine satellite DNA-based artificial chromosome across mammalian species. Chromosome Res, 1999, 7(1):3-7.
DeLise A M, Tuan R S. Electroporation-mediated DNA transfection of embryonic chick limb mesenchymal cells. Methods Mol Biol, 2000, 137:377-382.
Zimmer R, Verrinder Gibbins A M. Construction and characterization of a large-fragment chicken bacterial artificial chromosome library. Genomics, 1997, 42(2):217-226.
Brown D M, Chan Y J A, Desai P J, et al. Efficient sizeindependent chromosome delivery from yeast to cultured cell lines. Nucleic Acids Res, 2017, 45(7):e50.
Li L B, Chang K H, Wang P R, et al. Trisomy correction in down syndrome induced pluripotent stem cells. Cell Stem Cell, 2012, 11(5):615-619.
Matsumura H, Tada M, Otsuji T, et al. Targeted chromosome elimination from ES-somatic hybrid cells. Nat Methods, 2007, 4(1):23-25.
Mali P, Esvelt K M, Church G M. Cas9 as a versatile tool for engineering biology. Nat Methods, 2013, 10(10):957-963.
Zuo E W, Huo X N, Yao X, et al. CRISPR/Cas9-mediated targeted chromosome elimination. Genome Biol, 2017, 18(1):224..
Jiang W J, Zhao X J, Gabrieli T, et al. Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nat Commun, 2015, 6:8101.
Junnan, LU; Zhouqing, LUO; Shuangying, JIANG; Yue, SHEN; Yi, WU; Huanming, YANG; Yingjin, YUAN; and Junbiao, DAI
"Technologies for DNA Synthesis, Assembly, and Transplantation,"
Bulletin of Chinese Academy of Sciences (Chinese Version): Vol. 33
, Article 5.
Available at: https://bulletinofcas.researchcommons.org/journal/vol33/iss11/5