High-throughput, cost-effective verification of structural DNA assembly

Nucleic Acids Research

Volumn 42, Issue 4, 2014, Pages

  Dharmadi, Yandi ^a   Patel, Kedar ^a   Shapland, Elaine ^a   Hollis, Daniel ^a   Slaby, Todd ^a   Klinkner, Nicole ^a   Dean, Jed ^a   Chandran, Sunil S ^a  

^a Amyris Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLASMID DNA;

ARTICLE; AUTOMATED PATTERN RECOGNITION; CAPILLARY ELECTROPHORESIS; COMPUTER MODEL; COST EFFECTIVENESS ANALYSIS; DNA ASSEMBLY; GENE AMPLIFICATION; GENE CONSTRUCT; GENE SYNTHESIS; GENETIC ENGINEERING; HIGH THROUGHPUT SCREENING; MOLECULAR CLONING; PRIORITY JOURNAL; SYNTHETIC BIOLOGY;

ALGORITHMS; COMPUTER SIMULATION; DNA; DNA RESTRICTION ENZYMES; ELECTROPHORESIS, CAPILLARY; SEQUENCE ANALYSIS, DNA; SYNTHETIC BIOLOGY;

EID: 84895832249     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1088     Document Type: Article

References (30)

1. Kitney, R. and Freemont, P. (2012) Synthetic biology-the state of play. FEBS Lett., 586, 2029-2036.
2. Agapakis, C.M. and Silver, P.A. (2009) Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Mol. Biosyst., 5, 704-713.
3. Pasotti, L., Politi, N., Zucca, S., Cusella De Angelis, M.G. and Magni, P. (2012) Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices. PLoS ONE, 7, e39407.
4. Anderson, J.C., Dueber, J.E., Leguia, M., Wu, G.C., Goler, J.A., Arkin, A.P. and Keasling, J.D. (2010) BglBricks: a flexible standard for biological part assembly. J. Biol. Eng., 4, 1-1.
5. Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H.M. and Gennari, J.H. (2011) Standard biological parts knowledgebase. PLoS ONE, 6, e17005.
6. Gibson, D.G. (2009) Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res., 37, 6984-6990.
7. Ma, S., Tang, N. and Tian, J. (2012) DNA synthesis, assembly and applications in synthetic biology. Curr. Opin. Chem. Biol., 16, 260-267.
8. Jiang, X., Yang, J., Zhang, H., Zou, H., Wang, C. and Xian, M. (2012) In vitro assembly of multiple DNA fragments using successive hybridization. PLoS ONE, 7, e30267.
9. Quan, J. and Tian, J. (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS ONE, 4, e6441.
10. Schmid-Burgk, J.L., Xie, Z., Frank, S., Virreira Winter, S., Mitschka, S., Kolanus, W., Murray, A. and Benenson, Y. (2012) Rapid hierarchical assembly of medium-size DNA cassettes. Nucleic Acids Res., 40, e92.
11. Shao, Z. and Zhao, H. (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res., 37, e16.
12. Gibson, D.G., Benders, G.A., Axelrod, K.C., Zaveri, J., Algire, M.A., Moodie, M., Montague, M.G., Venter, J.C., Smith, H.O. and Hutchison, C.A. (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl Acad. Sci. USA, 105, 20404-20409.
13. Gibson, D.G., Young, L., Chuang, R.-Y., Venter, J.C., Hutchison, C.A. and Smith, H.O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods, 6, 343-345.
14. Constante, M., Grunberg, R. and Isalan, M. (2011) A biobrick library for cloning custom eukaryotic plasmids. PLoS ONE, 6, e23685.
15. Dean, F.B., Nelson, J.R., Giesler, T.L. and Lasken, R.S. (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res., 11, 1095-1099.
16. Maschke, H.E., Frenz, J., Belenkii, A., Karger, B.L. and Hancock, W.S. (1993) Ultrasensitive plasmid mapping by high performance capillary electrophoresis. Electrophoresis, 14, 509-514.
17. Peck, K., Wung, S.L., Chang, G.S., Yen, J.J. and Hsieh, Y.Z. (1997) Restriction mapping of genes by capillary electrophoresis with laser-induced fluorescence detection. Anal. Chem., 69, 1380-1384.
18. Strege, M. and Lagu, A. (1991) Separation of DNA restriction fragments by capillary electrophoresis using coated fused silica capillaries. Anal. Chem., 63, 1233-1236.
19. Entian, K.-D. and Kotter, P. (2007) Yeast genetic strain and plasmid collections. Method. Microbiol., 36, 629-666.
20. Yanisch-Perron, C., Vieira, J. and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene, 33, 103-119.
21. Sikorski, R.S. and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122, 19-27.
22. Ma, H., Kunes, S., Schatz, P.J. and Botstein, D. (1987) Plasmid construction by homologous recombination in yeast. Gene, 58, 201-216.
23. Manivasakam, P., Weber, S.C., McElver, J. and Schiestl, R.H. (1995) Micro-homology mediated PCR targeting in Saccharomyces cerevisiae. Nucleic Acids Res., 23, 2799-2800.
24. Oldenburg, K.R., Vo, K.T., Michaelis, S. and Paddon, C. (1997) Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res., 25, 451-452.
25. Gietz, R.D. and Woods, R.A. (2001) Genetic transformation of yeast. Biotechniques, 30, 816-820.
26. Bubeck, P., Winkler, M. and Bautsch, W. (1993) Rapid cloning by homologous recombination in vivo. Nucleic Acids Res., 21, 3601-3602.
27. Oliner, J.D., Kinzler, K.W. and Vogelstein, B. (1993) In vivo cloning of PCR products in E. coli. Nucleic Acids Res., 21, 5192-5197.
28. Zhu, D., Zhong, X., Tan, R., Chen, L., Huang, G., Li, J., Sun, X., Xu, L., Chen, J., Ou, Y. et al. (2010) High-throughput cloning of human liver complete open reading frames using homologous recombination in Escherichia coli. Anal. Biochem., 397, 162-167.
29. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res., 38, 234-236.
30. Ghosal, S. (2006) Electrokinetic flow and dispersion in capillary electrophoresis. Annu. Rev. Fluid Mech., 38, 309-338.