Next generation gene synthesis: From microarrays to genomes

Engineering in Life Sciences

Volumn 17, Issue 1, 2017, Pages 6-13

  Kuhn, Phillip ^a   Wagner, Katrin ^a   Heil, Korbinian ^a   Liss, Michael ^a   Netuschil, Nikolai ^a  

^a THERMO FISHER SCIENTIFIC   (Germany)

Author keywords

Cloning; Gene synthesis; Genome synthesis; Microarrays; Microfluidics; Oligonucleotides

Indexed keywords

BIOSYNTHESIS; CLONING; COST REDUCTION; DNA SEQUENCES; GENE ENCODING; MICROFLUIDICS; OLIGONUCLEOTIDES;

DE NOVO SYNTHESIS; DNA SEQUENCING; GENE ASSEMBLY; GENE SYNTHESIS; GENERATION TECHNIQUES; HIGH-THROUGHPUT SYNTHESIS; NOVEL TECHNIQUES;

MICROARRAYS;

OLIGONUCLEOTIDE;

ARRAY; COST ANALYSIS; DNA; GENE; GENETIC ANALYSIS; GENOME; RNA;

DNA MICROARRAY; GENE SYNTHESIS; GENOME; REVIEW;

EID: 84985912352     PISSN: 16180240     EISSN: 16182863     Source Type: Journal    
DOI: 10.1002/elsc.201600121     Document Type: Review

References (59)

1. Cameron, D. E., Bashor, C. M., Collins, J. J., A brief history of synthetic biology. Nat. Rev. Microbiol. 2014, 12, 381–390.
2. Notka, F., Liss, M. Wagner, R., Industrial scale gene synthesis. Methods Enzymol. 2011, 498, 247–275.
3. Beaucage, S. L., Caruthers, M. H., Deoxynucleoside phosphoramidites—a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedr. Lett. 1981, 22, 1859–1862.
4. Caruthers, M. H., Beaucage, S. L., Becker, C., Efcavitch, J. W. et al., Deoxyoligonucleotide synthesis via the phosphoramidite method. Gene Amplif. Anal. 1983, 3, 1–26.
5. Fodor, S. P., Read, J. L., Pirrung, M. C., Stryer, L. et al., Light-directed, spatially addressable parallel chemical synthesis. Science 1991, 251, 767–773.
6. Pease, A. C., Solas, D., Sullivan, E. J., Cronin, M. T. et al., Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. U S A 1994, 91, 5022–5026.
7. Singh-Gasson, S., Green, R. D., Yue, Y., Nelson, C., Blattner, F. et al., Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 1999, 17, 974–978.
8. Gao, X., LeProust, E., Zhang, H., Srivannavit, O. et al., A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res. 2001, 29, 4744–4750.
9. Egeland, R., Marken, F., Southern E., An electrochemical redox couple activitated by microelectrodes for confined chemical patterning of surfaces. Anal. Chem. 2002, 74, 1590–1596.
10. Ghindilis, A. L., Smith, M. W., Schwarzkopf, K. R., Roth, K. M. et al., CombiMatrix oligonucleotide arrays: Genotyping and gene expression assays employing electrochemical detection. Biosens. Bioelectron. 2007, 22, 1853–1860.
11. Blanchard, A. P., Kaiser, R. J., Hood, L. E., High-density oligonucleotide arrays. Biosens. Bioelectron. 1996, 11, 687–690.
12. Hughes, T. R., Mao, M., Jones, A. R., Burchard, J. et al., Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 2001, 19, 342–347.
13. Saaem, I., Ma, K. S., Marchi, A. N., LaBean, T. H., Tian, J. D., In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate. ACS Appl. Mater. Interface 2010, 2, 491–497.
14. Klein, J. C., Lajoie, M. J., Schwartz, J. J., Strauch, E. M. et al., Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Res. 2016, 44, e43.
15. Borovkov, A. Y., Loskutov, A. V., Robida, M. D., Day, K. M. et al., High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides. Nucleic Acids Res. 2010, 38, e180.
16. Kim, H., Jeong, J., Bang, D., Hierarchical gene synthesis using DNA microchip oligonucleotides, J. Biotechnol. 2011, 151, 319–324.
17. Lee, C. C., Snyder, T. M., Quake, S. R., A microfluidic oligonucleotide synthesizer. Nucleic Acid Res. 2010, 38, 2514–2521.
18. Kong, D. S., Carr, P. A., Chen, L., Zhang, S., Jacobson, J. M., Parallel gene synthesis in a microfluidic device. Nucleic Acid Res. 2007, 35, e61.
19. Quan, J., Saaem, I., Tang, N., Ma, S. et al., Parallel on-chip gene synthesis and application to optimization of protein expression. Nat. Biotechnol. 2011, 29, 449–452.
20. Banyai, W., Peck, B. J., Fernadez, A., Chen, S., Indermuhle, P., De novo synthesized gene libraries. US Patent Application 2015/0038373, 2015.
21. Tian, J. D., Gong, H., Sheng, N. J., Zhou, X. C., Gulari, E. et al., Accurate multiplex gene synthesis from programmable DNA microchips. Nature 2004, 432, 1050–1054.
22. Richmond, K. E., Li, M. H., Rodesch, M. J., Patel, M. et al., Amplification and assembly of chip-eluted DNA (AACED): A method for high-throughput gene synthesis. Nucleic Acids Res. 2004, 32, 5011–5018.
23. Zhou, X., Cai, S., Hong, A., You, Q. et al., Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucleic Acids Res. 2004, 32, 5409–5417.
24. Polz, M. F., Cavanaugh, C. M., Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64, 3724–3730.
25. Kosuri, S., Eroshenko, N., Leproust, E. M., Super, M. et al., Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat. Biotechnol. 2010, 28, 1295–1299.
26. Fuhrmann, M., Oertel, W., Berthold, P., Hegemann, P., Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage. Nucleic Acids Res. 2005, 33, e58.
27. Saaem, I., Ma, S., Quan, J., Tian, J., Error correction of microchip synthesized genes using Surveyor nuclease. Nucleic Acids Res. 2012, 40, e23.
28. Wan, W., Li, L., Xu, Q., Wang, Z., Yao, Y. et al., Error removal in microchip-synthesized DNA using immobilized MutS. Nucleic Acids Res. 2014, 42, e102.
29. Binkowski, B. F., Richmond, K. E., Kaysen, J., Sussman, M. R., Belshaw, P. J., Correcting errors in synthetic DNA through consensus shuffling. Nucleic Acids Res. 2005, 33, e55.
30. Carson, S., Wick, S. T., Carr, P. A., Wanunu, M., Aguilar, C. A., Direct analysis of gene synthesis reactions using solid-state nanopores. ACS Nano 2015, 9, 12417–12424.
31. Matzas, M., Stahler, P. F., Kefer, N., Siebelt, N. et al., High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat. Biotechnol. 2010, 28, 1291–1294.
32. Lee, H., Kim, H., Kim, S., Ryu, T. et al., A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform. Nat. Commun. 2015, 6, 6073.
33. Schwartz, J. J., Lee, C., Shendure, J., Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nat. Methods 2012, 9, 913–915.
34. Kim, H., Han, H., Ahn, J., Lee, J. et al., ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules. Nucleic Acids Res. 2012, 40, e140.
35. Padgett, K. A., Sorge, J. A., Creating seamless junctions independent of restriction sites in PCR cloning. Gene 1996, 168, 31–35.
36. Dietmaier, W., Fabry, S., Schmitt, R., DISEC-TRISEC: Di- and trinucleotide-sticky-end cloning of PCR-amplified DNA. Nucleic Acids Res. 1993, 21, 3603–3604.
37. Gibson, D. G., Benders, G. A., Axelrod, K. C., Zaveri, J. et al., One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl. Acad. Sci. U S A 2008, 105, 20404–20409.
38. Engler, C., Kandzia, R., Marillonnet, S., A one pot, one step, precision cloning method with high throughput capability. PLoS One 2008, 3, e3647.
39. Engler C, Marillonnet S., Golden gate cloning. Methods Mol. Biol. 2014, 1116, 119–131.
40. Chen, W. H., Qin, Z. J., Wang, J., Zhao, G. P., The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Res. 2013, 41, e93.
41. Aslanidis, C., de Jong, P. J., Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 1990, 18, 6069–6074.
42. Jones, D. H., Sakamoto, K., Vorce, R. L., Howard, B. H., DNA mutagenesis and recombination. Nature 1990, 344, 793–794.
43. Shuldiner, A. R., Scott, L. A., Roth, J., PCR-induced (ligase-free) subcloning: A rapid reliable method to subclone polymerase chain reaction (PCR) products. Nucleic Acids Res. 1990, 18, 1920.
44. Li, M. Z., Elledge, S. J., Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods 2007, 4, 251–256.
45. Gibson, D. G., Young, L., Chuang, R. Y., Venter, R. C. et al., Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 2009, 6, 343–345.
46. Geu-Flores, F., Nour-Eldin, H. H., Nielsen, M. T., Halkier, B. A., USER fusion: A rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 2007, 35, e55.
47. Quan, J., Tian, J., Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 2009, 4, e6441.
48. Zhang, Y., Werling, U., Edelmann, W., SLiCE: A novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res. 2012, 40, e55.
49. Ma, H., Kunes, S., Schatz, P. J., Botstein, D., Plasmid construction by homologous recombination in yeast. Gene 1987, 58, 201–216.
50. Shao, Z., Zhao, H., Zhao, H., DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res. 2009, 37, e16.
51. Gibson, D. G., Benders G. A., Andrews-Pfannkoch, C., Denisova, E. A. et al., Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008, 319, 1215–1220.
52. Kostylev, M., Otwell, A. E., Richardson, R. E., Suzuki, Y., Cloning should be simple: Escherichia coli DH5α-mediated assembly of multiple DNA fragments with short end homologies. PLoS One 2015, 10, e013746.
53. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N. et al., Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010, 329, 52–56.
54. Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S. et al., Total synthesis of a functional designer eukaryotic chromosome. Science 2014, 344, 55–58
55. Boeke, J., Chruch, G., Hessel, A., Kelley, N. et al., The Genome Project–Write. Science 2016, 353, 126–127.
56. Alvarado-Urbina, G., Sathe, G. M., Liu, W. C., Gillen, M. F. et al., Automated synthesis of gene fragments. Science 1981, 214, 270–274
57. Patwardhan, R. P., Lee, C., Litvin, O., Young, D. et al., High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 2009, 27, 1173–1175.
58. Smith, R. P., Taher, L., Patwardhan, R. P., Kim, M. J. et al., Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat. Genet. 2013, 45, 1021–1028.
59. Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P. et al., Programming circuitry for synthetic biology, Science 2016, 352, 48–50.