Hierarchical gene synthesis using DNA microchip oligonucleotides

Journal of Biotechnology

Volumn 151, Issue 4, 2011, Pages 319-324

  Kim, Hwangbeom ^a   Jeong, Jaehwan ^a   Bang, Duhee ^a  

^a Yonsei University   (South Korea)

Author keywords

DNA microchip; Gene synthesis; Synthetic biology

Indexed keywords

DNA ASSEMBLIES; DNA MICROCHIPS; DNA MOLECULES; DNA OLIGONUCLEOTIDES; DNA POLYMERASE GENES; GENE SYNTHESIS; HIERARCHICAL METHOD; SYNTHETIC BIOLOGY;

DNA; GENES; MICROPROCESSOR CHIPS; OLIGONUCLEOTIDES; SYNTHESIS (CHEMICAL);

NUCLEIC ACIDS;

DNA POLYMERASE; OLIGONUCLEOTIDE;

ARTICLE; DNA FLANKING REGION; DNA MICROARRAY; DPO4 GENE; GENE; GENE SEQUENCE; GENE SYNTHESIS; MOLECULAR SIZE; PFU GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STRUCTURAL GENE;

DNA; DNA-DIRECTED DNA POLYMERASE; GENES, SYNTHETIC; OLIGODEOXYRIBONUCLEOTIDES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 79951553139     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2011.01.004     Document Type: Article

References (22)

1. Bang D., Church G.M. Gene synthesis by circular assembly amplification. Nat. Methods 2008, 5:37-39.
2. Borovkov A.Y., Loskutov A.V., Robida M.D., Day K.M., Cano J.A., Le Olson T., Patel H., Brown K., Hunter P.D., Sykes K.F. High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides. Nucleic Acids Res. 2010.
3. Carr P.A., Church G.M. Genome engineering. Nat. Biotechnol. 2009, 27:1151-1162.
4. Cello J., Paul A.V., Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 2002, 297:1016-1018.
5. Coleman J.R., Papamichail D., Skiena S., Futcher B., Wimmer E., Mueller S. Virus attenuation by genome-scale changes in codon pair bias. Science 2008, 320:1784-1787.
6. Czar M.J., Anderson J.C., Bader J.S., Peccoud J. Gene synthesis demystified. Trends Biotechnol. 2009, 27:63-72.
7. Gibson D.G., Benders G.A., Andrews-Pfannkoch C., Denisova E.A., Baden-Tillson H., Zaveri J., Stockwell T.B., Brownley A., Thomas D.W., Algire M.A., et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008, 319:1215-1220.
8. Gibson D.G., Glass J.I., Lartigue C., Noskov V.N., Chuang R.Y., Algire M.A., Benders G.A., Montague M.G., Ma L., Moodie M.M., et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010, 329:52-56.
9. Hutchison C.A., Smith H.O., Pfannkoch C., Venter J.C. Cell-free cloning using phi29 DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:17332-17336.
10. Kodumal S.J., Patel K.G., Reid R., Menzella H.G., Welch M., Santi D.V. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:15573-15578.
11. Lee C.C., Snyder T.M., Quake S.R. A microfluidic oligonucleotide synthesizer. Nucleic Acids Res. 2010, 38:2514-2521.
12. LeProust E.M., Peck B.J., Spirin K., McCuen H.B., Moore B., Namsaraev E., Caruthers M.H. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res. 2010, 38:2522-2540.
13. Mueller S., Coleman J.R., Papamichail D., Ward C.B., Nimnual A., Futcher B., Skiena S., Wimmer E. Live attenuated influenza virus vaccines by computer-aided rational design. Nat. Biotechnol. 2010, 28:723-726.
14. Mueller S., Coleman J.R., Wimmer E. Putting synthesis into biology: a viral view of genetic engineering through de novo gene and genome synthesis. Chem. Biol. 2009, 16:337-347.
15. Richmond K.E., Li M.H., Rodesch M.J., Patel M., Lowe A.M., Kim C., Chu L.L., Venkataramaian N., Flickinger S.F., Kaysen J., et al. Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis. Nucleic Acids Res. 2004, 32:5011-5018.
16. Smith H.O., Hutchison C.A., Pfannkoch C., Venter J.C. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:15440-15445.
17. Stemmer W.P., Crameri A., Ha K.D., Brennan T.M., Heyneker H.L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 1995, 164:49-53.
18. Tian J., Gong H., Sheng N., Zhou X., Gulari E., Gao X., Church G. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 2004, 432:1050-1054.
19. Tian J., Ma K., Saaem I. Advancing high-throughput gene synthesis technology. Mol. Biosyst. 2009, 5:714-722.
20. Tumpey T.M., Basler C.F., Aguilar P.V., Zeng H., Solorzano A., Swayne D.E., Cox N.J., Katz J.M., Taubenberger J.K., Palese P., et al. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 2005, 310:77-80.
21. Welch M., Govindarajan S., Ness J.E., Villalobos A., Gurney A., Minshull J., Gustafsson C. Design parameters to control synthetic gene expression in Escherichia coli. PLoS One 2009, 4:e7002.
22. Zhou X., Cai S., Hong A., You Q., Yu P., Sheng N., Srivannavit O., Muranjan S., Rouillard J.M., Xia Y., et al. Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucleic Acids Res. 2004, 32:5409-5417.