Developments in the tools and methodologies of synthetic biology

Frontiers in Bioengineering and Biotechnology

Volumn 2, Issue NOV, 2014, Pages

  Kelwick, Richard ^a   MacDonald, James T ^a   Webb, Alexander J ^a   Freemont, Paul ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Design cycle; Engineering biology; Standardization; Synthetic biology; Tools

Indexed keywords

BIOLOGICAL SYSTEMS; STANDARDIZATION; TOOLS;

BIOLOGICAL DESIGN; BODY OF KNOWLEDGE; DESIGN CYCLE; ENGINEERING PRINCIPLES; FORWARD DESIGNS; RATIONAL DESIGN; SCIENTIFIC FIELDS; SYNTHETIC BIOLOGY;

BIOLOGY;

EID: 85043549520     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2014.00060     Document Type: Review

References (242)

1. Acevedo-Rocha, C. G., Fang, G., Schmidt, M., Ussery, D. W., and Danchin, A. (2013). From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet. 29, 273-279. doi:10.1016/j.tig.2012.11.001
2. Agapakis, C. M. (2013). Designing synthetic biology. ACS Synth. Biol. 3, 121-128. doi:10.1021/sb4001068
3. Agapakis, C. M., Boyle, P. M., and Silver, P. A. (2012). Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat. Chem. Biol. 8, 527-535. doi:10.1038/nchembio.975
4. Anderson, J., Strelkowa, N., Stan, G. B., Douglas, T., Savulescu, J., Barahona, M., et al. (2012). Engineering and ethical perspectives in synthetic biology. Rigorous, robust and predictable designs, public engagement and a modern ethical framework are vital to the continued success of synthetic biology. EMBO Rep. 13, 584-590. doi:10.1038/embor.2012.81
5. Anderson, J. C., Dueber, J. E., Leguia, M., Wu, G. C., Goler, J. A., Arkin, A. P., et al. (2010). BglBricks: a flexible standard for biological part assembly. J. Biol. Eng. 4, 1. doi:10.1186/1754-1611-4-1
6. Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2, 0028. doi:10.1038/msb4100073
7. Andronescu, M., Fejes, A. P., Hutter, F., Hoos, H. H., and Condon, A. (2004). A new algorithm for RNA secondary structure design. J. Mol. Biol. 336, 607-624. doi:10.1016/j.jmb.2003.12.041
8. Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., et al. (2014). Total synthesis of a functional designer eukaryotic chromosome. Science 344, 55-58. doi:10.1126/science.1249252
9. Arkin, A. (2008). Setting the standard in synthetic biology. Nat. Biotechnol. 26, 771-774. doi:10.1038/nbt0708-771
10. Arkin, A. P. (2013). A wise consistency: engineering biology for conformity, reliability, predictability. Curr. Opin. Chem. Biol. 17, 893-901. doi:10.1016/j.cbpa.2013.09.012
11. Arpino, J. A., Hancock, E. J., Anderson, J., Barahona, M., Stan, G. B., Papachristodoulou, A., et al. (2013). Tuning the dials of synthetic biology. Microbiology 159, 1236-1253. doi:10.1099/mic.0.067975-0
12. Atlas, J. C., Nikolaev, E. V., Browning, S. T., and Shuler, M. L. (2008). Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication. IET Syst. Biol. 2, 369-382. doi:10.1049/iet-syb:20070079
13. Aw, R., and Polizzi, K. M. (2013). Can too many copies spoil the broth? Microb. Cell Fact. 12, 128. doi:10.1186/1475-2859-12-128
14. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., et al. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712. doi:10.1126/science.1138140
15. Barrick, J. E., and Breaker, R. R. (2007). The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 8, R239. doi:10.1186/gb-2007-8-11-r239
16. Bartosiak-Jentys, J., Hussein, A. H., Lewis, C. J., and Leak, D. J. (2013). Modular system for assessment of glycosyl hydrolase secretion in Geobacillus thermoglucosidasius. Microbiology 159, 1267-1275. doi:10.1099/mic.0.066332-0
17. Basiji, D. A., Ortyn, W. E., Liang, L., Venkatachalam, V., and Morrissey, P. (2007). Cellular image analysis and imaging by flow cytometry. Clin. Lab. Med. 27, 653-670. doi:10.1016/j.cll.2007.05.008
18. Benedetto, A., Accetta, G., Fujita, Y., and Charras, G. (2014). Spatiotemporal control of gene expression using microfluidics. Lab. Chip 14, 1336-1347. doi:10.1039/c3lc51281a
19. Berla, B. M., Saha, R., Immethun, C. M., Maranas, C. D., Moon, T. S., and Pakrasi, H. B. (2013). Synthetic biology of cyanobacteria: unique challenges and opportunities. Front. Microbiol. 4:246. doi:10.3389/fmicb.2013.00246
20. Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., and Marraffini, L. A. (2013). Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41, 7429-7437. doi:10.1093/nar/gkt520
21. Blount, B. A., Weenink, T., Vasylechko, S., and Ellis, T. (2012). Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS ONE 7:e33279. doi:10.1371/journal.pone.0033279
22. Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., et al. (2009). Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509-1512. doi:10.1126/science.1178811
23. Boehm, C. R., Freemont, P. S., and Ces, O. (2013). Design of a prototype flow microreactor for synthetic biology in vitro. Lab. Chip 13, 3426-3432. doi:10.1039/c3lc50231g
24. Bonde, M. T., Klausen, M. S., Anderson, M. V., Wallin, A. I., Wang, H. H., and Sommer, M. O. (2014). MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res. 42, W408-W415. doi:10.1093/nar/gku428
25. Bower, A. G., McClintock, M. K., and Fong, S. S. (2010). Synthetic biology: a foundation for multi-scale molecular biology. Bioeng. Bugs 1, 309-312. doi:10.4161/bbug.1.5.12391
26. Cachat, E., and Davies, J. A. (2011). Application of synthetic biology to regenerative medicine. J. Bioeng. Biomed. Sci. S2:003. doi:10.4172/2155-9538.S2-003
27. Calvert, J. (2012). Ownership and sharing in synthetic biology: a/'diverse ecology/' of the open and the proprietary[quest]. BioSocieties 7, 169-187. doi:10.1057/biosoc.2012.3
28. Canton, B., Labno, A., and Endy, D. (2008). Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26, 787-793. doi:10.1038/nbt1413
29. Carlson, R. (2009). The changing economics of DNA synthesis. Nat. Biotechnol. 27, 1091-1094. Available at: http://www.synthesis.cc/cgi-bin/mt/mt-search.cgi?blog_id=1&tag=CarlsonCurves&limit=20 doi:10.1038/nbt1209-1091
30. Caschera, F., and Noireaux, V. (2014). Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. Biochimie 99, 162-168. doi:10.1016/j.biochi.2013.11.025
31. Casini, A., Christodoulou, G., Freemont, P. S., Baldwin, G. S., Ellis, T., and MacDonald, J. T. (2014). R2oDNA designer: computational design of biologically neutral synthetic DNA Sequences. ACS Synth. Biol. 3, 525-528. doi:10.1021/sb4001323
32. Casini, A., MacDonald, J. T., Jonghe, J. D., Christodoulou, G., Freemont, P. S., Baldwin, G. S., et al. (2013). One-pot DNA construction for synthetic biology: the modular overlap-directed assembly with linkers (MODAL) strategy. Nucleic Acids Res. 42, e7. doi:10.1093/nar/gkt915
33. Cereghino, J. (2000). Heterologous protein expression in the methylotrophic yeast Pichia pastoris. FEMS Microbiol. Rev. 24, 45-66. doi:10.1016/s0168-6445(99)00029-7
34. Chao, R., Yuan, Y., and Zhao, H. (2014). Recent advances in DNA assembly technologies. FEMS Yeast Res. doi:10.1111/1567-1364.12171
35. Chappell, J., Jensen, K., and Freemont, P. S. (2013). Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res. 41, 3471-3481. doi:10.1093/nar/gkt052
36. Chen, I. A., Roberts, R. W., and Szostak, J. W. (2004). The emergence of competition between model protocells. Science 305, 1474-1476. doi:10.1126/science.1100757
37. Chin, J. X., Chung, B. K., and Lee, D. Y. (2014). Codon optimization online (COOL): a web-based multi-objective optimization platform for synthetic gene design. Bioinformatics 30, 2210-2212. doi:10.1093/bioinformatics/btu192
38. Chiyoda, S., Yamato, K. T., and Kohchi, T. (2014). Plastid transformation of sporelings and suspension-cultured cells from the liverwort Marchantia polymorpha L. Methods Mol. Biol. 1132, 439-447. doi:10.1007/978-1-62703-995-6_30
39. Chizzolini, F., Forlin, M., Cecchi, D., and Mansy, S. S. (2013). Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter strength. ACS Synth. Biol 3, 363-371. doi:10.1021/sb4000977
40. Cho, M., Soo Oh, S., Nie, J., Stewart, R., Eisenstein, M., Chambers, J., et al. (2013). Quantitative selection and parallel characterization of aptamers. Proc. Natl. Acad. Sci. U.S.A. 110, 18460-18465. doi:10.1073/pnas.1315866110
41. Choi, H. J., and Montemagno, C. D. (2005). Artificial organelle: ATP synthesis from cellular mimetic polymersomes. Nano Lett. 5, 2538-2542. doi:10.1021/nl051896e
42. Choi, S. L., Rha, E., Lee, S. J., Kim, H., Kwon, K., Jeong, Y. S., et al. (2013). Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits. ACS Synth. Biol. 3, 163-171. doi:10.1021/sb400112u
43. Chung, B. K., and Lee, D. Y. (2012). Computational codon optimization of synthetic gene for protein expression. BMC Syst. Biol. 6:134. doi:10.1186/1752-0509-6-134
44. Cohen, S. N., Chang, A. C., Boyer, H. W., and Helling, R. B. (1973). Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. U.S.A. 70, 3240-3244. doi:10.1073/pnas.70.11.3240
45. Collins, F. S., and Tabak, L. A. (2014). Policy: NIH plans to enhance reproducibility. Nature 505, 612-613. doi:10.1038/505612a
46. Colloms, S. D., Merrick, C. A., Olorunniji, F. J., Stark, W. M., Smith, M. C., Osbourn, A., et al. (2014). Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res. 42, e23. doi:10.1093/nar/gkt1101
47. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823. doi:10.1126/science.1231143
48. Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., et al. (2010). Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 26, 925-931. doi:10.1093/bioinformatics/btq063
49. Cregg, J. M., Cereghino, J. L., Shi, J., and Higgins, D. R. (2000). Recombinant protein expression in Pichia pastoris. Mol. Biotechnol. 16, 23-52. doi:10.1385/mb:16:1:23
50. Cregg, J. M., Tolstorukov, I., Kusari, A., Sunga, J., Madden, K., and Chappell, T. (2009). Chapter 13 expression in the yeast Pichia pastoris. Meth. Enzymol. 463, 169-189. doi:10.1016/s0076-6879(09)63013-5
51. Csete, M. E., and Doyle, J. C. (2002). Reverse engineering of biological complexity. Science 295, 1664-1669. doi:10.1126/science.1069981
52. Danchin, A., and Sekowska, A. (2014). The logic of metabolism and its fuzzy consequences. Environ. Microbiol. 16, 19-28. doi:10.1111/1462-2920.12270
53. Davis, J. H., Rubin, A. J., and Sauer, R. T. (2011). Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 39, 1131-1141. doi:10.1093/nar/gkq810
54. de Kok, S., Stanton, L. H., Slaby, T., Durot, M., Holmes, V. F., Patel, K. G., et al. (2014). Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth. Biol. 3, 97-106. doi:10.1021/sb4001992
55. Delebecque, C. J., Lindner, A. B., Silver, P. A., and Aldaye, F. A. (2011). Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470-474. doi:10.1126/science.1206938
56. Depaoli, H. C., Borland, A. M., Tuskan, G. A., Cushman, J. C., and Yang, X. (2014). Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. J. Exp. Bot. 65, 3381-3393. doi:10.1093/jxb/eru038
57. Dewall, M. T., and Cheng, D. W. (2011). The minimal genome: a metabolic and environmental comparison. Brief. Funct. Genomics 10, 312-315. doi:10.1093/bfgp/elr030
58. Díaz, M., Herrero, M., García, L. A., and Quirós, C. (2010). Application of flow cytometry to industrial microbial bioprocesses. Biochem. Eng. J. 48, 385-407. doi:10.1016/j.bej.2009.07.013
59. Douglas, C. M. W., and Stemerding, D. (2014). Challenges for the European governance of synthetic biology for human health. Life Sci. Soc. Policy 10, 6. doi:10.1186/s40504-014-0006-7
60. Douglas, S. M., Dietz, H., Liedl, T., Hogberg, B., Graf, F., and Shih, W. M. (2009). Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414-418. doi:10.1038/nature08016
61. Dueber, J. E., Wu, G. C., Malmirchegini, G. R., Moon, T. S., Petzold, C. J., Ullal, A. V., et al. (2009). Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 27, 753-759. doi:10.1038/nbt.1557
62. Dutton, P. L., and Moser, C. C. (2011). Engineering enzymes. Faraday Discuss. 148, 443. doi:10.1039/c005523a
63. Dymond, J., and Boeke, J. (2012). The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Bioeng. Bugs 3, 168-171. doi:10.4161/bbug.19543
64. Ellefson, J. W., Meyer, A. J., Hughes, R. A., Cannon, J. R., Brodbelt, J. S., and Ellington, A. D. (2014). Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat. Biotechnol. 32, 97-101. doi:10.1038/nbt.2714
65. Ellington, A. D., and Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822. doi:10.1038/346818a0
66. Ellis, B. L., Hirsch, M. L., Porter, S. N., Samulski, R. J., and Porteus, M. H. (2013). Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by food and drug administration-approved drugs. Gene Ther. 20, 35-42. doi:10.1038/gt.2011.211
67. Ellis, T., Adie, T., and Baldwin, G. S. (2011). DNA assembly for synthetic biology: from parts to pathways and beyond. Integr. Biol. (Camb.) 3, 109-118. doi:10.1039/c0ib00070a
68. Elowitz, M. B., and Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338. doi:10.1038/35002125
69. Endy, D. (2005). Foundations for engineering biology. Nature 438, 449-453. doi:10.1038/nature04342
70. Engler, C., Kandzia, R., and Marillonnet, S. (2008). A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3:e3647. doi:10.1371/journal.pone.0003647
71. Engler, C., and Marillonnet, S. (2011). Generation of families of construct variants using golden gate shuffling. Methods Mol. Biol. 729, 167-181. doi:10.1007/978-1-61779-065-2_11
72. Engler, C., and Marillonnet, S. (2013). Combinatorial DNA assembly using golden gate cloning. Methods Mol. Biol. 1073, 141-156. doi:10.1007/978-1-62703-625-2_12
73. Esvelt, K. M., Carlson, J. C., and Liu, D. R. (2011). A system for the continuous directed evolution of biomolecules. Nature 472, 499-503. doi:10.1038/nature09929
74. Fletcher, J. M., Harniman, R. L., Barnes, F. R., Boyle, A. L., Collins, A., Mantell, J., et al. (2013). Self-assembling cages from coiled-coil peptide modules. Science 340, 595-599. doi:10.1126/science.1233936
75. Frow, E., and Calvert, J. (2013). Opening up the future(s) of synthetic biology. Futures 48, 32-43. doi:10.1016/j.futures.2013.03.001
76. Fu, J., Liu, M., Liu, Y., Woodbury, N. W., and Yan, H. (2012). Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. J. Am. Chem. Soc. 134, 5516-5519. doi:10.1021/ja300897h
77. Fu, J., Yang, Y. R., Johnson-Buck, A., Liu, M., Liu, Y., Walter, N. G., et al. (2014). Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. Nat. Nanotechnol. 9, 531-536. doi:10.1038/nnano.2014.100
78. Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., et al. (2014). The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotechnol. 32, 545-550. doi:10.1038/nbt.2891
79. Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H. M., and Gennari, J. H. (2011). Standard biological parts knowledgebase. PLoS ONE 6:e17005. doi:10.1371/journal.pone.0017005
80. Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muniz-Rascado, L., Solano-Lira, H., et al. (2011). RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res. 39, D98-D105. doi:10.1093/nar/gkq1110
81. Gan, R., and Jewett, M. C. (2014). A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthesis. Biotechnol. J. 9, 641-651. doi:10.1002/biot.201300545
82. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342. doi:10.1038/35002131
83. Gibson, D. G. (2011). Enzymatic assembly of overlapping DNA fragments. Meth. Enzymol. 498, 349-361. doi:10.1016/B978-0-12-385120-8.00015-2
84. Gibson, D. G., Benders, G. A., Andrews-Pfannkoch, C., Denisova, E. A., Baden-Tillson, H., Zaveri, J., et al. (2008). Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215-1220. doi:10.1126/science.1151721
85. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., et al. (2010a). Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-56. doi:10.1126/science.1190719
86. Gibson, D. G., Smith, H. O., Hutchison, C. A. III, Venter, J. C., and Merryman, C. (2010b). Chemical synthesis of the mouse mitochondrial genome. Nat. Methods 7, 901-903. doi:10.1038/nmeth.1515
87. Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A. III, and Smith, H. O. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345. doi:10.1038/nmeth.1318
88. Glass, J. I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M. R., Maruf, M., et al. (2006). Essential genes of a minimal bacterium. Proc. Natl. Acad. Sci. U.S.A. 103, 425-430. doi:10.1073/pnas.0510013103
89. Guye, P., Li, Y., Wroblewska, L., Duportet, X., and Weiss, R. (2013). Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res. 41, e156. doi:10.1093/nar/gkt605
90. Hamilton, S. R., and Gerngross, T. U. (2007). Glycosylation engineering in yeast: the advent of fully humanized yeast. Curr. Opin. Biotechnol. 18, 387-392. doi:10.1016/j.copbio.2007.09.001
91. Hammer, D. A., and Kamat, N. P. (2012). Towards an artificial cell. FEBS Lett. 586, 2882-2890. doi:10.1016/j.febslet.2012.07.044
92. Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., and Yan, H. (2011). DNA origami with complex curvatures in three-dimensional space. Science 332, 342-346. doi:10.1126/science.1202998
93. Hansen, A. S., and O'Shea, E. K. (2013). Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol. Syst. Biol. 9, 704. doi:10.1038/msb.2013.56
94. Harwood, C. R., Pohl, S., Smith, W., and Wipat, A. (2013). Bacillus subtilis: model Gram-positive synthetic biology chassis. Comput. Sci. 40, 87-117. doi:10.1016/b978-0-12-417029-2.00004-2
95. Heider, S. A. E., Wolf, N., Hofemeier, A., Peters-Wendisch, P., and Wendisch, V. F. (2014). Optimization of the IPP precursor supply for the production of lycopene, decaprenoxanthin and astaxanthin by Corynebacterium glutamicum. Front. Bioeng. Biotechnol. 2:28. doi:10.3389/fbioe.2014.00028
96. Heidorn, T., Camsund, D., Huang, H. H., Lindberg, P., Oliveira, P., Stensjo, K., et al. (2011). Synthetic biology in cyanobacteria engineering and analyzing novel functions. Meth. Enzymol. 497, 539-579. doi:10.1016/B978-0-12-385075-1.00024-X
97. Heigwer, F., Kerr, G., and Boutros, M. (2014). E-CRISP: fast CRISPR target site identification. Nat. Methods 11, 122-123. doi:10.1038/nmeth.2812
98. Heinemann, M., and Panke, S. (2006). Synthetic biology-putting engineering into biology. Bioinformatics 22, 2790-2799. doi:10.1093/bioinformatics/btl469
99. Hillson, N. J., Rosengarten, R. D., and Keasling, J. D. (2012). j5 DNA assembly design automation software. ACS Synth. Biol. 1, 14-21. doi:10.1021/sb2000116
100. Hiroe, A., Tsuge, K., Nomura, C. T., Itaya, M., and Tsuge, T. (2012). Rearrangement of gene order in the phaCAB operon leads to effective production of ultrahigh-molecular-weight poly[(R)-3-hydroxybutyrate] in genetically engineered Escherichia coli. Appl. Environ. Microbiol. 78, 3177-3184. doi:10.1128/AEM.07715-11
101. Hodgman, C. E., and Jewett, M. C. (2013). Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis. Biotechnol. Bioeng. 110, 2643-2654. doi:10.1002/bit.24942
102. Hong, S. H., Kwon, Y.-C., and Jewett, M. C. (2014). Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Front. Chem. 2:34. doi:10.3389/fchem.2014.00034
103. Howorka, S. (2011). Rationally engineering natural protein assemblies in nanobiotechnology. Curr. Opin. Biotechnol. 22, 485-491. doi:10.1016/j.copbio.2011.05.003
104. Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., et al. (2011). Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348-353. doi:10.1126/science.1205822
105. Itaya, M., Fujita, K., Kuroki, A., and Tsuge, K. (2008). Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat. Methods 5, 41-43. doi:10.1038/nmeth1143
106. Iwata, T., Kaneko, S., Shiwa, Y., Enomoto, T., Yoshikawa, H., and Hirota, J. (2013). Bacillus subtilis genome vector-based complete manipulation and reconstruction of genomic DNA for mouse transgenesis. BMC Genomics 14:300. doi:10.1186/1471-2164-14-300
107. Iyer, S., Karig, D. K., Norred, S. E., Simpson, M. L., and Doktycz, M. J. (2013). Multi-input regulation and logic with T7 promoters in cells and cell-free systems. PLoS ONE 8:e78442. doi:10.1371/journal.pone.0078442
108. Jefferson, C., Lentzos, F., and Marris, C. (2014). Synthetic biology and biosecurity: challenging the "myths". Front. Public Health 2:115. doi:10.3389/fpubh.2014.00115
109. Jenison, R. D., Gill, S. C., Pardi, A., and Polisky, B. (1994). High-resolution molecular discrimination by RNA. Science 263, 1425-1429. doi:10.1126/science.7510417
110. Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Rothlisberger, D., Zanghellini, A., et al. (2008). De novo computational design of retro-aldol enzymes. Science 319, 1387-1391. doi:10.1126/science.1152692
111. Karig, D. K., Iyer, S., Simpson, M. L., and Doktycz, M. J. (2012). Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res. 40, 3763-3774. doi:10.1093/nar/gkr1191
112. Kelly, J. R., Rubin, A. J., Davis, J. H., Ajo-Franklin, C. M., Cumbers, J., Czar, M. J., et al. (2009). Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng. 3, 4. doi:10.1186/1754-1611-3-4
113. Keren, L., Zackay, O., Lotan-Pompan, M., Barenholz, U., Dekel, E., Sasson, V., et al. (2013). Promoters maintain their relative activity levels under different growth conditions. Mol. Syst. Biol. 9, 701. doi:10.1038/msb.2013.59
114. Khalil, A. S., and Collins, J. J. (2010). Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367-379. doi:10.1038/nrg2775
115. King, N. P., Bale, J. B., Sheffler, W., McNamara, D. E., Gonen, S., Gonen, T., et al. (2014). Accurate design of co-assembling multi-component protein nanomaterials. Nature 510, 103-108. doi:10.1038/nature13404
116. King, N. P., Sheffler, W., Sawaya, M. R., Vollmar, B. S., Sumida, J. P., Andre, I., et al. (2012). Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171-1174. doi:10.1126/science.1219364
117. Kitney, R., and Freemont, P. (2012). Synthetic biology-the state of play. FEBS Lett. 586, 2029-2036. doi:10.1016/j.febslet.2012.06.002
118. Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T. B., Montelione, G. T., et al. (2012). Principles for designing ideal protein structures. Nature 491, 222-227. doi:10.1038/nature11600
119. Kouprina, N., and Larionov, V. (2008). Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc. 3, 371-377. doi:10.1038/nprot.2008.5
120. Landrain, T., Meyer, M., Perez, A. M., and Sussan, R. (2013). Do-it-yourself biology: challenges and promises for an open science and technology movement. Syst. Synth. Biol. 7, 115-126. doi:10.1007/s11693-013-9116-4
121. Lawrence, A. D., Frank, S., Newnham, S., Lee, M. J., Brown, I. R., Xue, W. F., et al. (2014). Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synth. Biol. 3, 454-465. doi:10.1021/sb4001118
122. Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., et al. (2011). ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Meth. Enzymol. 487, 545-574. doi:10.1016/B978-0-12-381270-4.00019-6
123. Li, M. Z., and Elledge, S. J. (2007). Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods 4, 251-256. doi:10.1038/nmeth1010
124. Liang, J. C., Bloom, R. J., and Smolke, C. D. (2011). Engineering biological systems with synthetic RNA molecules. Mol. Cell 43, 915-926. doi:10.1016/j.molcel.2011.08.023
125. Lienert, F., Lohmueller, J. J., Garg, A., and Silver, P. A. (2014). Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol. 15, 95-107. doi:10.1038/nrm3738
126. Lin, B., and Levchenko, A. (2012). Microfluidic technologies for studying synthetic circuits. Curr. Opin. Chem. Biol. 16, 307-317. doi:10.1016/j.cbpa.2012.04.012
127. Lin, Q., Jia, B., Mitchell, L. A., Luo, J., Yang, K., Zeller, K. I., et al. (2014). RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synth. Biol. doi:10.1021/sb500241e
128. Linshiz, G., Stawski, N., Poust, S., Bi, C., Keasling, J. D., and Hillson, N. J. (2013). PaR-PaR laboratory automation platform. ACS Synth. Biol. 2, 216-222. doi:10.1021/sb300075t
129. Liu, C. C., Qi, L., Lucks, J. B., Segall-Shapiro, T. H., Wang, D., Mutalik, V. K., et al. (2012). An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nat. Methods 9, 1088-1094. doi:10.1038/nmeth.2184
130. Lobban, P. E., and Kaiser, A. D. (1973). Enzymatic end-to end joining of DNA molecules. J. Mol. Biol. 78, 453-471. doi:10.1016/0022-2836(73)90468-3
131. Lou, C., Stanton, B., Chen, Y. J., Munsky, B., and Voigt, C. A. (2012). Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat. Biotechnol. 30, 1137-1142. doi:10.1038/nbt.2401
132. Lu, W.-C., and Ellington, A. D. (2014). Design and Selection of a Synthetic Operon. ACS Synth. Biol. 3, 410-415. doi:10.1021/sb400160m
133. MacDonald, J. T., Barnes, C., Kitney, R. I., Freemont, P. S., and Stan, G. B. (2011). Computational design approaches and tools for synthetic biology. Integr. Biol. (Camb.) 3, 97-108. doi:10.1039/c0ib00077a
134. Mahfouz, M. M., Li, L., Shamimuzzaman, M., Wibowo, A., Fang, X., and Zhu, J. K. (2011). De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc. Natl. Acad. Sci. U.S.A. 108, 2623-2628. doi:10.1073/pnas.1019533108
135. Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., et al. (2013). CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838. doi:10.1038/nbt.2675
136. Marchisio, M. A. (2014). In silico design and in vivo implementation of yeast gene Boolean gates. J. Biol. Eng. 8, 6. doi:10.1186/1754-1611-8-6
137. Marchisio, M. A., and Stelling, J. (2009). Computational design tools for synthetic biology. Curr. Opin. Biotechnol. 20, 479-485. doi:10.1016/j.copbio.2009.08.007
138. Markham, N. R., and Zuker, M. (2008). UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol. 453, 3-31. doi:10.1007/978-1-60327-429-6_1
139. Marples, B., Scott, S. D., Hendry, J. H., Embleton, M. J., Lashford, L. S., and Margison, G. P. (2000). Development of synthetic promoters for radiation-mediated gene therapy. Gene Ther. 7, 511-517. doi:10.1038/sj.gt.3301116
140. Marris, C., and Rose, N. (2010). Open engagement: exploring public participation in the biosciences. PLoS Biol. 8:e1000549. doi:10.1371/journal.pbio.1000549
141. Moe-Behrens, G. H., Davis, R., and Haynes, K. A. (2013). Preparing synthetic biology for the world. Front. Microbiol. 4:5. doi:10.3389/fmicb.2013.00005
142. Morbitzer, R., Romer, P., Boch, J., and Lahaye, T. (2010). Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors. Proc. Natl. Acad. Sci. U.S.A. 107, 21617-21622. doi:10.1073/pnas.1013133107
143. Moscou, M. J., and Bogdanove, A. J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501. doi:10.1126/science.1178817
144. Muller, K., Siegel, D., Rodriguez Jahnke, F., Gerrer, K., Wend, S., Decker, E. L., et al. (2014a). A red light-controlled synthetic gene expression switch for plant systems. Mol. Biosyst. 10, 1679-1688. doi:10.1039/c3mb70579j
145. Muller, K., Zurbriggen, M. D., and Weber, W. (2014b). Control of gene expression using a red-and far-red light-responsive bi-stable toggle switch. Nat. Protoc. 9, 622-632. doi:10.1038/nprot.2014.038
146. Murphy, K. C. (1998). Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 180, 2063-2071.
147. Murphy, K. C., and Campellone, K. G. (2003). Lambda red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli. BMC Mol. Biol. 4:11. doi:10.1186/1471-2199-4-11
148. Mushtaq, M. Y., Verpoorte, R., and Kim, H. K. (2013). Zebrafish as a model for systems biology. Biotechnol. Genet. Eng. Rev. 29, 187-205. doi:10.1080/02648725.2013.801238
149. Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q. A., et al. (2013a). Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 10, 354-360. doi:10.1038/nmeth.2404
150. Mutalik, V. K., Guimaraes, J. C., Cambray, G., Mai, Q. A., Christoffersen, M. J., Martin, L., et al. (2013b). Quantitative estimation of activity and quality for collections of functional genetic elements. Nat. Methods 10, 347-353. doi:10.1038/nmeth.2403
151. Na, D., and Lee, D. (2010). RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 26, 2633-2634. doi:10.1093/bioinformatics/btq458
152. Narayanan, K., and Chen, Q. (2011). Bacterial artificial chromosome mutagenesis using recombineering. J. Biomed. Biotechnol. 2011, 971296. doi:10.1155/2011/971296
153. Nirenberg, M. W., and Matthaei, J. H. (1961). The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc. Natl. Acad. Sci. U.S.A. 47, 1588-1602. doi:10.1073/pnas.47.10.1588
154. Nishiyama, T. (2000). Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by shuttle mutagenesis. DNA Res. 7, 9-17. doi:10.1093/dnares/7.1.9
155. O'Brien, E. J., Lerman, J. A., Chang, R. L., Hyduke, D. R., and Palsson, B. O. (2013). Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol. Syst. Biol. 9, 693. doi:10.1038/msb.2013.52
156. Ohtani, N., Hasegawa, M., Sato, M., Tomita, M., Kaneko, S., and Itaya, M. (2012). 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. 7, 867-876. doi:10.1002/biot.201100396
157. Olson, E. J., Hartsough, L. A., Landry, B. P., Shroff, R., and Tabor, J. J. (2014). Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat. Methods 11, 449-455. doi:10.1038/nmeth.2884
158. O'Reilly, L. P., Luke, C. J., Perlmutter, D. H., Silverman, G. A., and Pak, S. C. (2014). C. elegans in high-throughput drug discovery. Adv. Drug Deliv. Rev. 6, 247-253. doi:10.1016/j.addr.2013.12.001
159. Padilla, J. E., Colovos, C., and Yeates, T. O. (2001). Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl. Acad. Sci. U.S.A. 98, 2217-2221. doi:10.1073/pnas.041614998
160. Paige, J. S., Wu, K. Y., and Jaffrey, S. R. (2011). RNA mimics of green fluorescent protein. Science 333, 642-646. doi:10.1126/science.1207339
161. Penchovsky, R., and Breaker, R. R. (2005). Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat. Biotechnol. 23, 1424-1433. doi:10.1038/nbt1155
162. Piyasena, M. E., and Graves, S. W. (2014). The intersection of flow cytometry with microfluidics and microfabrication. Lab. Chip 14, 1044-1059. doi:10.1039/c3lc51152a
163. Pothoulakis, G., Ceroni, F., Reeve, B., and Ellis, T. (2014). The spinach RNA aptamer as a characterization tool for synthetic biology. ACS Synth. Biol. 3, 182-187. doi:10.1021/sb400089c
164. Preston, B. (2013). Synthetic biology as red herring. Stud. Hist. Philos. Biol. Biomed. Sci. 44, 649-659. doi:10.1016/j.shpsc.2013.05.012
165. Purnick, P. E., and Weiss, R. (2009). The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410-422. doi:10.1038/nrm2698
166. Qi, L., Haurwitz, R. E., Shao, W., Doudna, J. A., and Arkin, A. P. (2012). RNA processing enables predictable programming of gene expression. Nat. Biotechnol. 30, 1002-1006. doi:10.1038/nbt.2355
167. Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., et al. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183. doi:10.1016/j.cell.2013.02.022
168. Quan, J., and Tian, J. (2009). Circular polymerase extension cloning of complex gene libraries and pathways. PLoS ONE 4:e6441. doi:10.1371/journal.pone.0006441
169. Quan, J., and Tian, J. (2011). Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat. Protoc. 6, 242-251. doi:10.1038/nprot.2010.181
170. Quinn, J., Beal, J., Bhatia, S., Cai, P., Chen, J., Clancy, K., et al. (2013). Synthetic biology open language visual (SBOL visual), version 1.0.0, BBF RFC #93. doi:1721.1/78249
171. Radeck, J., Kraft, K., Bartels, J., Cikovic, T., Durr, F., Emenegger, J., et al. (2013). The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. J. Biol. Eng. 7, 29. doi:10.1186/1754-1611-7-29
172. Rajagopal, K., and Schneider, J. P. (2004). Self-assembling peptides and proteins for nanotechnological applications. Curr. Opin. Struct. Biol. 14, 480-486. doi:10.1016/j.sbi.2004.06.006
173. Redemann, S., Schloissnig, S., Ernst, S., Pozniakowsky, A., Ayloo, S., Hyman, A. A., et al. (2011). Codon adaptation-based control of protein expression in C. elegans. Nat. Methods 8, 250-252. doi:10.1038/nmeth.1565
174. Reeve, B., Hargest, T., Gilbert, C., and Ellis, T. (2014). Predicting translation initiation rates for designing synthetic biology. Front. Bioeng. Biotechnol. 2:1. doi:10.3389/fbioe.2014.00001
175. Rhodius, V. A., and Mutalik, V. K. (2010). Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc. Natl. Acad. Sci. U.S.A. 107, 2854-2859. doi:10.1073/pnas.0915066107
176. Rhodius, V. A., Mutalik, V. K., and Gross, C. A. (2012). Predicting the strength of UP-elements and full-length E. coli sigmaE promoters. Nucleic Acids Res. 40, 2907-2924. doi:10.1093/nar/gkr1190
177. Rodrigo, G., and Jaramillo, A. (2013). AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth. Biol. 2, 230-236. doi:10.1021/sb300084h
178. Roehner, N., and Myers, C. J. (2013). A methodology to annotate systems biology markup language models with the synthetic biology open language. ACS Synth. Biol. 3, 57-66. doi:10.1021/sb400066m
179. Rokke, G., Korvald, E., Pahr, J., Oyas, O., and Lale, R. (2014). BioBrick assembly standards and techniques and associated software tools. Methods Mol. Biol. 1116, 1-24. doi:10.1007/978-1-62703-764-8_1
180. Ross, J. A., Ellis, M. J., Hossain, S., and Haniford, D. B. (2013). Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA 19, 670-684. doi:10.1261/rna.037747.112
181. Roth, A., and Breaker, R. R. (2009). The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem. 78, 305-334. doi:10.1146/annurev.biochem.78.070507.135656
182. Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302. doi:10.1038/nature04586
183. Rothlisberger, D., Khersonsky, O., Wollacott, A. M., Jiang, L., Dechancie, J., Betker, J., et al. (2008). Kemp elimination catalysts by computational enzyme design. Nature 453, 190-195. doi:10.1038/nature06879
184. Rouillard, J. M., Lee, W., Truan, G., Gao, X., Zhou, X., and Gulari, E. (2004). Gene2Oligo: oligonucleotide design for in vitro gene synthesis. Nucleic Acids Res. 32, W176-W180. doi:10.1093/nar/gkh401
185. Salis, H. M. (2011). The ribosome binding site calculator. Meth. Enzymol. 498, 19-42. doi:10.1016/B978-0-12-385120-8.00002-4
186. Salis, H. M., Mirsky, E. A., and Voigt, C. A. (2009). Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27, 946-950. doi:10.1038/nbt.1568
187. Sander, J. D., and Joung, J. K. (2014). CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347-355. doi:10.1038/nbt.2842
188. Schaefer, D. G., and Zryd, J.-P. (1997). Efficient gene targeting in the moss Physcomitrella patens. Plant J. 11, 1195-1206. doi:10.1046/j.1365-313X.1997.11061195.x
189. Schark, M. (2012). Synthetic biology and the distinction between organisms and machines. Environ. Values 21, 19-41. doi:10.3197/096327112x13225063227943
190. Sefah, K., Yang, Z., Bradley, K. M., Hoshika, S., Jimenez, E., Zhang, L., et al. (2013). In vitro selection with artificial expanded genetic information systems. Proc. Natl. Acad. Sci. U.S.A. 111, 1449-1454. doi:10.1073/pnas.1311778111
191. Seo, S. W., Yang, J. S., Kim, I., Yang, J., Min, B. E., Kim, S., et al. (2013). Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab. Eng. 15, 67-74. doi:10.1016/j.ymben.2012.10.006
192. Sharma, N., Jung, C. H., Bhalla, P. L., and Singh, M. B. (2014). RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha. PLoS One 9:e97497. doi:10.1371/journal.pone.0097497
193. Shi, Z., Wedd, A. G., and Gras, S. L. (2013). Parallel in vivo DNA assembly by recombination: experimental demonstration and theoretical approaches. PLoS ONE 8:e56854. doi:10.1371/journal.pone.0056854
194. Shin, J., and Noireaux, V. (2012). An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synth. Biol. 1, 29-41. doi:10.1021/sb200016s
195. Shuler, M. L., Foley, P., and Atlas, J. (2012). Modeling a minimal cell. Methods Mol. Biol. 881, 573-610. doi:10.1007/978-1-61779-827-6_20
196. Silva-Rocha, R., Martinez-Garcia, E., Calles, B., Chavarria, M., Arce-Rodriguez, A., De Las Heras, A., et al. (2013). The standard European vector architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res. 41, D666-D675. doi:10.1093/nar/gks1119
197. Sinclair, J. C., Davies, K. M., Venien-Bryan, C., and Noble, M. E. (2011). Generation of protein lattices by fusing proteins with matching rotational symmetry. Nat. Nanotechnol. 6, 558-562. doi:10.1038/nnano.2011.122
198. Sitaraman, K., Esposito, D., Klarmann, G., Le Grice, S. F., Hartley, J. L., and Chatterjee, D. K. (2004). A novel cell-free protein synthesis system. J. Biotechnol. 110, 257-263. doi:10.1016/j.jbiotec.2004.02.014
199. Song, C. W., Lee, J., and Lee, S. Y. (2014). Genome engineering and gene expression control for bacterial strain development. Biotechnol. J. doi:10.1002/biot.201400057
200. Song, Y., Sauret, A., and Cheung Shum, H. (2013). All-aqueous multiphase microfluidics. Biomicrofluidics 7, 61301. doi:10.1063/1.4827916
201. Speer, M. A., and Richard, T. L. (2011). Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits. J. Biol. Eng. 5, 17. doi:10.1186/1754-1611-5-17
202. Stanton, B. C., Nielsen, A. A., Tamsir, A., Clancy, K., Peterson, T., and Voigt, C. A. (2014). Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat. Chem. Biol. 10, 99-105. doi:10.1038/nchembio.1411
203. Stricker, J., Cookson, S., Bennett, M. R., Mather, W. H., Tsimring, L. S., and Hasty, J. (2008). A fast, robust and tunable synthetic gene oscillator. Nature 456, 516-519. doi:10.1038/nature07389
204. Suess, B., Fink, B., Berens, C., Stentz, R., and Hillen, W. (2004). A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res. 32, 1610-1614. doi:10.1093/nar/gkh321
205. Sukhorukov, G. B., Rogach, A. L., Zebli, B., Liedl, T., Skirtach, A. G., Kohler, K., et al. (2005). Nanoengineered polymer capsules: tools for detection, controlled delivery, and site-specific manipulation. Small 1, 194-200. doi:10.1002/smll.200400075
206. Sun, Z. Z., Hayes, C. A., Shin, J., Caschera, F., Murray, R. M., and Noireaux, V. (2013a). Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. J. Vis. Exp. 79:e50762. doi:10.3791/50762
207. Sun, Z. Z., Yeung, E., Hayes, C. A., Noireaux, V., and Murray, R. M. (2013b). Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synth. Biol 3, 387-397. doi:10.1021/sb400131a
208. Szeto, K., Reinholt, S. J., Duarte, F. M., Pagano, J. M., Ozer, A., Yao, L., et al. (2014). High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. Anal. Bioanal. Chem. 406, 2727-2732. doi:10.1007/s00216-014-7661-7
209. Tang, J., and Breaker, R. R. (1997). Rational design of allosteric ribozymes. Chem. Biol. 4, 453-459. doi:10.1016/S1074-5521(97)90197-6
210. Tantillo, D. J., Chen, J., and Houk, K. N. (1998). Theozymes and compuzymes: theoretical models for biological catalysis. Curr. Opin. Chem. Biol. 2, 743-750. doi:10.1016/S1367-5931(98)80112-9
211. Tomlinson, M. L., Hendry, A. E., and Wheeler, G. N. (2012). Chemical genetics and drug discovery in Xenopus. Methods Mol. Biol. 917, 155-166. doi:10.1007/978-1-61779-992-1_9
212. Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., and Silver, P. A. (2014a). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic Acids Res. 42, 681-689. doi:10.1093/nar/gkt860
213. Torella, J. P., Lienert, F., Boehm, C. R., Chen, J. H., Way, J. C., and Silver, P. A. (2014b). Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications. Nat. Protoc. 9, 2075-2089. doi:10.1038/nprot.2014.145
214. Tracy, B. P., Gaida, S. M., and Papoutsakis, E. T. (2010). Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr. Opin. Biotechnol. 21, 85-99. doi:10.1016/j.copbio.2010.02.006
215. Trubitsyna, M., Michlewski, G., Cai, Y., Elfick, A., and French, C. E. (2014). PaperClip: rapid multi-part DNA assembly from existing libraries. Nucleic Acids Res. 42, e154. doi:10.1093/nar/gku829
216. Tuerk, C., and Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510. doi:10.1126/science.2200121
217. Uchida, M., Klem, M. T., Allen, M., Suci, P., Flenniken, M., Gillitzer, E., et al. (2007). Biological containers: protein cages as multifunctional nanoplatforms. Adv. Mater. Weinheim 19, 1025-1042. doi:10.1002/adma.200601168
218. Villalobos, A., Ness, J. E., Gustafsson, C., Minshull, J., and Govindarajan, S. (2006). Gene designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 7:285. doi:10.1186/1471-2105-7-285
219. Vogl, T., Hartner, F. S., and Glieder, A. (2013). New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris. Curr. Opin. Biotechnol. 24, 1094-1101. doi:10.1016/j.copbio.2013.02.024
220. Walsh, G. (2010). Post-translational modifications of protein biopharmaceuticals. Drug Discov. Today 15, 773-780. doi:10.1016/j.drudis.2010.06.009
221. Walter, N. G., and Bustamante, C. (2014). Introduction to single molecule imaging and mechanics: seeing and touching molecules one at a time. Chem. Rev. 114, 3069-3071. doi:10.1021/cr500059w
222. Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., et al. (2009). Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894-898. doi:10.1038/nature08187
223. Wang, Y., and Zhang, Y. H. (2009). Cell-free protein synthesis energized by slowly-metabolized maltodextrin. BMC Biotechnol. 9:58. doi:10.1186/1472-6750-9-58
224. Way, J. C., Collins, J. J., Keasling, J. D., and Silver, P. A. (2014). Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 157, 151-161. doi:10.1016/j.cell.2014.02.039
225. White, R. M., Cech, J., Ratanasirintrawoot, S., Lin, C. Y., Rahl, P. B., Burke, C. J., et al. (2011). DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature 471, 518-522. doi:10.1038/nature09882
226. Wittmann, A., and Suess, B. (2012). Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett. 586, 2076-2083. doi:10.1016/j.febslet.2012.02.038
227. Woolfson, D. N., and Mahmoud, Z. N. (2010). More than just bare scaffolds: towards multi-component and decorated fibrous biomaterials. Chem. Soc. Rev. 39, 3464-3479. doi:10.1039/c0cs00032a
228. Wright, O., Delmans, M., Stan, G. B., and Ellis, T. (2014). GeneGuard: a modular plasmid system designed for biosafety. ACS Synth. Biol. doi:10.1021/sb500234s
229. Wright, O., Stan, G. B., and Ellis, T. (2013). Building-in biosafety for synthetic biology. Microbiology 159, 1221-1235. doi:10.1099/mic.0.066308-0
230. Xu, J., Sigworth, F. J., and Lavan, D. A. (2010). Synthetic protocells to mimic and test cell function. Adv. Mater. 22, 120-127. doi:10.1002/adma.200901945
231. Xu, P., Vansiri, A., Bhan, N., and Koffas, M. A. (2012). ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth. Biol. 1, 256-266. doi:10.1021/sb300016b
232. Yang, J., and Reth, M. (2012). Drosophila S2 Schneider cells: a useful tool for rebuilding and redesigning approaches in synthetic biology. Methods Mol. Biol. 813, 331-341. doi:10.1007/978-1-61779-412-4_20
233. Ye, H., Aubel, D., and Fussenegger, M. (2013). Synthetic mammalian gene circuits for biomedical applications. Curr. Opin. Chem. Biol. 17, 910-917. doi:10.1016/j.cbpa.2013.10.006
234. Zaccai, N. R., Chi, B., Thomson, A. R., Boyle, A. L., Bartlett, G. J., Bruning, M., et al. (2011). A de novo peptide hexamer with a mutable channel. Nat. Chem. Biol. 7, 935-941. doi:10.1038/nchembio.692
235. Zadeh, J. N., Wolfe, B. R., and Pierce, N. A. (2011). Nucleic acid sequence design via efficient ensemble defect optimization. J. Comput. Chem. 32, 439-452. doi:10.1002/jcc.21633
236. Zaghloul, T., and Doi, R. (1987). In vitro expression of a Tn9-derived chloramphenicol acetyltransferase gene fusion by using a Bacillus subtilis system. J. Bacteriol. 169, 1212-1216.
237. Zanghellini, A., Jiang, L., Wollacott, A. M., Cheng, G., Meiler, J., Althoff, E. A., et al. (2006). New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 15, 2785-2794. doi:10.1110/ps.062353106
238. Zhang, F., and Keasling, J. (2011). Biosensors and their applications in microbial metabolic engineering. Trends Microbiol. 19, 323-329. doi:10.1016/j.tim.2011.05.003
239. Zhang, Y., Werling, U., and Edelmann, W. (2012). SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res. 40, e55. doi:10.1093/nar/gkr1288
240. Zhao, Y., Wang, S., and Zhu, J. (2011). A multi-step strategy for BAC recombineering of large DNA fragments. Int J Biochem Mol Biol 2, 199-206. Available from http://www.ijbmb.org/files/IJBMB1104005.pdf
241. Zimmerman, S. B., Little, J. W., Oshinsky, C. K., and Gellert, M. (1967). Enzymatic joining of DNA strands: a novel reaction of diphosphopyridine nucleotide. Proc. Natl. Acad. Sci. U.S.A. 57, 1841-1848. doi:10.1073/pnas.57.6.1841
242. Zuleta, I. A., Aranda-Diaz, A., Li, H., and El-Samad, H. (2014). Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat. Methods 11, 443-448. doi:10.1038/nmeth.2879