메뉴 건너뛰기




Volumn 9, Issue 1, 2017, Pages

Synthetic DNA synthesis and assembly: Putting the synthetic in synthetic biology

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

EID: 85009090143     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a023812     Document Type: Article
Times cited : (289)

References (80)
  • 3
    • 0032499868 scopus 로고    scopus 로고
    • Gene synthesis by an LCR-based approach: High-level production of leptin-l54 using synthetic gene in Escherichia coli
    • Au, LC, Yang FY, Yang WJ, Lo SH, Kao CF. 1998. Gene synthesis by an LCR-based approach: High-level production of leptin-l54 using synthetic gene in Escherichia coli. Biochem Biophys Res Commun 248: 200–203.
    • (1998) Biochem Biophys Res Commun , vol.248 , pp. 200-203
    • Au, L.C.1    Yang, F.Y.2    Yang, W.J.3    Lo, S.H.4    Kao, C.F.5
  • 5
    • 84957058205 scopus 로고    scopus 로고
    • Antisense transcription as a tool to tune gene expression
    • Brophy, JA, Voigt CA. 2016. Antisense transcription as a tool to tune gene expression. Mol Syst Biol 12: 854.
    • (2016) Mol Syst Biol , vol.12 , pp. 854
    • Brophy, J.A.1    Voigt, C.A.2
  • 6
    • 84859589886 scopus 로고    scopus 로고
    • Genetic switchboard for synthetic biology applications
    • Callura, JM, Cantor CR, Collins JJ. 2012. Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci 109: 5850–5855.
    • (2012) Proc Natl Acad Sci , vol.109 , pp. 5850-5855
    • Callura, J.M.1    Cantor, C.R.2    Collins, J.J.3
  • 8
    • 79953169546 scopus 로고    scopus 로고
    • A brief review of DNA and RNA chemical synthesis
    • Caruthers, MH. 2011. A brief review of DNA and RNA chemical synthesis. Biochem Soc Trans 39: 575–580.
    • (2011) Biochem Soc Trans , vol.39 , pp. 575-580
    • Caruthers, M.H.1
  • 9
    • 0037106052 scopus 로고    scopus 로고
    • High throughput parallel synthesis of oligonucleotides with 1536 channel synthesizer
    • Cheng, JY, Chen HH, Kao YS, Kao WC, Peck K. 2002. High throughput parallel synthesis of oligonucleotides with 1536 channel synthesizer. Nucleic Acids Res 30: e93.
    • (2002) Nucleic Acids Res , vol.30
    • Cheng, J.Y.1    Chen, H.H.2    Kao, Y.S.3    Kao, W.C.4    Peck, K.5
  • 13
    • 0024995923 scopus 로고
    • A rapid method for the construction of synthetic genes using the polymerase chain reaction
    • Dillon, PJ, Rosen CA. 1990. A rapid method for the construction of synthetic genes using the polymerase chain reaction. BioTechniques 9: 298–300.
    • (1990) Biotechniques , vol.9 , pp. 298-300
    • Dillon, P.J.1    Rosen, C.A.2
  • 15
    • 84913594397 scopus 로고    scopus 로고
    • Genome editing. The new frontier of genome engineering with CRISPR-Cas9
    • Doudna, JA, Charpentier E. 2014. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346: 1258096.
    • (2014) Science , vol.346
    • Doudna, J.A.1    Charpentier, E.2
  • 16
    • 0242275926 scopus 로고
    • Depurination as a yield decreasing mechanism in oligodeoxynucleotide synthesis
    • Efcavitch, JW, Heiner C. 1985. Depurination as a yield decreasing mechanism in oligodeoxynucleotide synthesis. Nucleosides Nucleotides 4: 267–267.
    • (1985) Nucleosides Nucleotides , vol.4 , pp. 267-268
    • Efcavitch, J.W.1    Heiner, C.2
  • 17
    • 56649114274 scopus 로고    scopus 로고
    • A one pot, one step, precision cloning method with high throughput capability
    • Engler, C, Kandzia R, Marillonnet S. 2008. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3: e3647.
    • (2008) Plos ONE , vol.3
    • Engler, C.1    Kandzia, R.2    Marillonnet, S.3
  • 19
    • 28644447881 scopus 로고    scopus 로고
    • Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage
    • Fuhrmann, M, Oertel W, Berthold P, Hegemann P. 2005. Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage. Nucleic Acids Res 33: e58.
    • (2005) Nucleic Acids Res , vol.33
    • Fuhrmann, M.1    Oertel, W.2    Berthold, P.3    Hegemann, P.4
  • 21
    • 73349139923 scopus 로고    scopus 로고
    • Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
    • Gibson, DG. 2009. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res 37: 6984–6990.
    • (2009) Nucleic Acids Res , vol.37 , pp. 6984-6990
    • Gibson, D.G.1
  • 22
    • 79957471219 scopus 로고    scopus 로고
    • Enzymatic assembly of overlapping DNA fragments
    • Gibson, DG. 2011a. Enzymatic assembly of overlapping DNA fragments. Methods Enzymol 498: 349–361.
    • (2011) Methods Enzymol , vol.498 , pp. 349-361
    • Gibson, D.G.1
  • 23
    • 84857658214 scopus 로고    scopus 로고
    • Gene and genome construction in yeast
    • (ed. Ausubel FM et al.), Chapter 3, Unit 3.22. Wiley
    • Gibson, DG. 2011b. Gene and genome construction in yeast. In Current protocols in molecular biology (ed. Ausubel FM et al.), Chapter 3, Unit 3.22. Wiley
    • (2011) Current Protocols in Molecular Biology
    • Gibson, D.G.1
  • 24
    • 84858374402 scopus 로고    scopus 로고
    • Oligonucleotide assembly in yeast to produce synthetic DNA fragments
    • Hoboken, NJ., Gibson DG. 2012. Oligonucleotide assembly in yeast to produce synthetic DNA fragments. Methods Mol Biol 852: 11–21.
    • (2012) Methods Mol Biol , vol.852 , pp. 11-21
    • Hoboken, N.J.1    Gibson, D.G.2
  • 29
    • 84886824017 scopus 로고    scopus 로고
    • Rapid, modular and reliable construction of complex mammalian gene circuits
    • Guye, P, Li Y, Wroblewska L, Duportet X, Weiss R. 2013. Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res 41: e156.
    • (2013) Nucleic Acids Res , vol.41
    • Guye, P.1    Li, Y.2    Wroblewska, L.3    Duportet, X.4    Weiss, R.5
  • 32
    • 0017697097 scopus 로고
    • Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin
    • Itakura, K, Hirose T, Crea R, Riggs AD, Heyneker HL, Bolivar F, Boyer HW. 1977. Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. Science 198: 1056–1063.
    • (1977) Science , vol.198 , pp. 1056-1063
    • Itakura, K.1    Hirose, T.2    Crea, R.3    Riggs, A.D.4    Heyneker, H.L.5    Bolivar, F.6    Boyer, H.W.7
  • 33
    • 0025759897 scopus 로고
    • Polymerase chain reaction–mediated gene synthesis: Synthesis of a gene coding for isozyme c of horseradish peroxidase
    • Jayaraman, K, Fingar SA, Shah J, Fyles J. 1991. Polymerase chain reaction–mediated gene synthesis: Synthesis of a gene coding for isozyme c of horseradish peroxidase. Proc Natl Acad Sci 88: 4084–4088.
    • (1991) Proc Natl Acad Sci , vol.88 , pp. 4084-4088
    • Jayaraman, K.1    Fingar, S.A.2    Shah, J.3    Fyles, J.4
  • 38
    • 8144226497 scopus 로고    scopus 로고
    • Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster
    • Kodumal, SJ, Patel KG, Reid R, Menzella HG, Welch M, Santi DV. 2004. Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc Natl Acad Sci 101: 15573–15578.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 15573-15578
    • Kodumal, S.J.1    Patel, K.G.2    Reid, R.3    Menzella, H.G.4    Welch, M.5    Santi, D.V.6
  • 39
    • 84899696363 scopus 로고    scopus 로고
    • Large-scale de novo DNA synthesis: Technologies and applications
    • Kosuri, S, Church GM. 2014. Large-scale de novo DNA synthesis: Technologies and applications. Nat Method 11: 499–507.
    • (2014) Nat Method , vol.11 , pp. 499-507
    • Kosuri, S.1    Church, G.M.2
  • 40
    • 78650021707 scopus 로고    scopus 로고
    • Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
    • Kosuri, S, Eroshenko N, Leproust EM, Super M, Way J, Li JB, Church GM. 2010. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol 28: 1295–1299.
    • (2010) Nat Biotechnol , vol.28 , pp. 1295-1299
    • Kosuri, S.1    Eroshenko, N.2    Leproust, E.M.3    Super, M.4    Way, J.5    Li, J.B.6    Church, G.M.7
  • 43
    • 33847608289 scopus 로고    scopus 로고
    • Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
    • Li, MZ, Elledge SJ. 2007. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Method 4: 251–256.
    • (2007) Nat Method , vol.4 , pp. 251-256
    • Li, M.Z.1    Elledge, S.J.2
  • 44
    • 84865283376 scopus 로고    scopus 로고
    • DNA synthesis, assembly and applications in synthetic biology
    • Ma, S, Tang N, Tian J. 2012. DNA synthesis, assembly and applications in synthetic biology. Curr Opin Chem Biol 16: 260–267.
    • (2012) Curr Opin Chem Biol , vol.16 , pp. 260-267
    • Ma, S.1    Tang, N.2    Tian, J.3
  • 49
    • 68149136937 scopus 로고    scopus 로고
    • Circular polymerase extension cloning of complex gene libraries and pathways
    • Quan, J, Tian J. 2009. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS ONE 4: e6441.
    • (2009) Plos ONE , vol.4
    • Quan, J.1    Tian, J.2
  • 50
    • 79955773387 scopus 로고    scopus 로고
    • Parallel on-chip gene synthesis and application to optimization of protein expression
    • Quan, J, Saaem I, Tang N, Ma S, Negre N, Gong H, White KP, Tian J. 2011. Parallel on-chip gene synthesis and application to optimization of protein expression. Nat Biotechnol 29: 449–452.
    • (2011) Nat Biotechnol , vol.29 , pp. 449-452
    • Quan, J.1    Saaem, I.2    Tang, N.3    Ma, S.4    Negre, N.5    Gong, H.6    White, K.P.7    Tian, J.8
  • 53
    • 84888605243 scopus 로고    scopus 로고
    • Synthesis ofDNA/RNA and their analogs via phosphoramidite and H-phosphonate chemistries
    • Roy, S, Caruthers M. 2013. Synthesis ofDNA/RNA and their analogs via phosphoramidite and H-phosphonate chemistries. Molecules 18: 14268–14284.
    • (2013) Molecules , vol.18 , pp. 14268-14284
    • Roy, S.1    Caruthers, M.2
  • 54
    • 84973325042 scopus 로고    scopus 로고
    • Synthetic mixed-signal computation in living cells
    • Rubens, JR, Selvaggio G, Lu TK. 2016. Synthetic mixed-signal computation in living cells. Nat Commun 7: 11658.
    • (2016) Nat Commun , vol.7 , pp. 11658
    • Rubens, J.R.1    Selvaggio, G.2    Lu, T.K.3
  • 55
    • 77952312451 scopus 로고    scopus 로고
    • In situ synthesis ofDNA microarrayon functionalized cyclic olefin copolymer substrate
    • Saaem, I, Ma KS, Marchi AN, LaBean TH, Tian J. 2010. In situ synthesis ofDNA microarrayon functionalized cyclic olefin copolymer substrate. ACS Appl Mater Interfaces 2: 491–497.
    • (2010) ACS Appl Mater Interfaces , vol.2 , pp. 491-497
    • Saaem, I.1    Ma, K.S.2    Marchi, A.N.3    Labean, T.H.4    Tian, J.5
  • 56
    • 84856939965 scopus 로고    scopus 로고
    • Error correction of microchip synthesized genes using Surveyor nuclease
    • Saaem, I, Ma S, Quan J, Tian J. 2012. Error correction of microchip synthesized genes using Surveyor nuclease. Nucleic Acids Res 40: e23.
    • (2012) Nucleic Acids Res , vol.40
    • Saaem, I.1    Ma, S.2    Quan, J.3    Tian, J.4
  • 57
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis, HM, Mirsky EA, Voigt CA. 2009. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27: 946–950.
    • (2009) Nat Biotechnol , vol.27 , pp. 946-950
    • Salis, H.M.1    Mirsky, E.A.2    Voigt, C.A.3
  • 58
    • 84899704095 scopus 로고    scopus 로고
    • The rise of a digital immune system
    • Schatz, MC, Phillippy AM. 2012. The rise of a digital immune system. GigaScience 1: 4.
    • (2012) Gigascience , vol.1 , pp. 4
    • Schatz, M.C.1    Phillippy, A.M.2
  • 60
    • 84866128726 scopus 로고    scopus 로고
    • Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules
    • Schwartz, JJ, Lee C, Shendure J. 2012.Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nat Method 9: 913–915.
    • (2012) Nat Method , vol.9 , pp. 913-915
    • Schwartz, J.J.1    Lee, C.2    Shendure, J.3
  • 61
    • 0017281959 scopus 로고
    • Total synthesis of the structural gene for the precursor of a tyrosine suppressor transfer RNA from Escherichia coli. 7. Enzymatic joining of the chemically synthesized segments to form a DNA duplex corresponding to the nucleotide sequence 1-26
    • Sekiya, T, Besmer P, Takeya T, Khorana HG. 1976. Total synthesis of the structural gene for the precursor of a tyrosine suppressor transfer RNA from Escherichia coli. 7. Enzymatic joining of the chemically synthesized segments to form a DNA duplex corresponding to the nucleotide sequence 1-26. J Biol Chem 251: 634–641.
    • (1976) J Biol Chem , vol.251 , pp. 634-641
    • Sekiya, T.1    Besmer, P.2    Takeya, T.3    Khorana, H.G.4
  • 63
    • 0029776496 scopus 로고    scopus 로고
    • Kinetic studies on depurination and detritylation of CPG-bound intermediates during oligonucleotide synthesis
    • Septak, M. 1996. Kinetic studies on depurination and detritylation of CPG-bound intermediates during oligonucleotide synthesis. Nucleic Acids Res 24: 3053–3058.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3053-3058
    • Septak, M.1
  • 64
    • 45149118469 scopus 로고    scopus 로고
    • Engineering, BioBrick vectors from BioBrick parts
    • Shetty, RP, Endy D, Knight TF Jr. 2008. Engineering, BioBrick vectors from BioBrick parts. J Biol Eng 2: 5.
    • (2008) J Biol Eng , vol.2 , pp. 5
    • Shetty, R.P.1    Endy, D.2    Knight, T.F.3
  • 66
    • 0347364647 scopus 로고    scopus 로고
    • Generating a synthetic genome by whole genome assembly: WX174 bacteriophage from synthetic oligonucleotides
    • Smith HO, Hutchison CA III, Pfannkoch C, Venter JC. 2003. Generating a synthetic genome by whole genome assembly: wX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci 100: 15440–15445.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 15440-15445
    • Smith, H.O.1    Hutchison, C.2    Pfannkoch, C.3    Venter, J.C.4
  • 67
    • 84940774152 scopus 로고    scopus 로고
    • Advances in synthetic dynamic circuits design: Using novel synthetic parts to engineer new generations of gene oscillations
    • Sowa, SW, Gelderman G, Contreras LM. 2015. Advances in synthetic dynamic circuits design: Using novel synthetic parts to engineer new generations of gene oscillations. Curr Opin Biotechnol 36: 161–167.
    • (2015) Curr Opin Biotechnol , vol.36 , pp. 161-167
    • Sowa, S.W.1    Gelderman, G.2    Contreras, L.M.3
  • 68
    • 0028784138 scopus 로고
    • Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
    • Stemmer, WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. 1995. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164: 49–53.
    • (1995) Gene , vol.164 , pp. 49-53
    • Stemmer, W.P.1    Crameri, A.2    Ha, K.D.3    Brennan, T.M.4    Heyneker, H.L.5
  • 69
    • 84953334273 scopus 로고    scopus 로고
    • Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins
    • Tang, NC, Chilkoti A. 2016. Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins. Nat Mater 15: 419–424.
    • (2016) Nat Mater , vol.15 , pp. 419-424
    • Tang, N.C.1    Chilkoti, A.2
  • 70
    • 84860803588 scopus 로고    scopus 로고
    • Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca
    • Temme, K, Zhao D, Voigt CA. 2012. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci 109: 7085–7090.
    • (2012) Proc Natl Acad Sci , vol.109 , pp. 7085-7090
    • Temme, K.1    Zhao, D.2    Voigt, C.A.3
  • 71
    • 11144247743 scopus 로고    scopus 로고
    • Accurate multiplex gene synthesis from programmable DNA microchips
    • Tian, J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G. 2004. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432: 1050–1054.
    • (2004) Nature , vol.432 , pp. 1050-1054
    • Tian, J.1    Gong, H.2    Sheng, N.3    Zhou, X.4    Gulari, E.5    Gao, X.6    Church, G.7
  • 72
    • 84907021721 scopus 로고    scopus 로고
    • Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications
    • Torella, JP, Lienert F, Boehm CR, Chen JH, Way JC, Silver PA. 2014. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications. Nat Protoc 9: 2075–2089.
    • (2014) Nat Protoc , vol.9 , pp. 2075-2089
    • Torella, J.P.1    Lienert, F.2    Boehm, C.R.3    Chen, J.H.4    Way, J.C.5    Silver, P.A.6
  • 79
    • 17044455338 scopus 로고    scopus 로고
    • Two-step total gene synthesis method
    • Young, L, Dong Q. 2004. Two-step total gene synthesis method. Nucleic Acids Res 32: e59.
    • (2004) Nucleic Acids Res , vol.32
    • Young, L.1    Dong, Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.