Abstract
The yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp and can be as long as 200 nucleotides in length to produce kilobase-sized synthetic DNA molecules. A protocol for designing the oligonucleotides to be assembled, transforming them into yeast, and confirming their assembly is described here. This straightforward scheme for assembling chemically synthesized oligonucleotides can be a useful tool for building synthetic DNA molecules.
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References
Agarwal, K. L., Buchi, H., Caruthers, M. H., Gupta, N., Khorana, H. G., Kleppe, K., Kumar, A., Ohtsuka, E., Rajbhandary, U. L., Van de Sande, J. H., Sgaramella, V., Weber, H., and Yamada, T. (1970) Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast, Nature 227, 27–34.
Reese, C. B. (2005) Oligo- and poly-nucleotides: 50 years of chemical synthesis, Org. Biomol. Chem. 3, 3851–3868.
Xiong, A. S., Peng, R. H., Zhuang, J., Gao, F., Li, Y., Cheng, Z. M., and Yao, Q. H. (2008) Chemical gene synthesis: strategies, softwares, error corrections, and applications, FEMS Microbiol. Rev. 32, 522–540.
Xiong, A. S., Peng, R. H., Zhuang, J., Liu, J. G., Gao, F., Chen, J. M., Cheng, Z. M., and Yao, Q. H. (2008) Non-polymerase-cycling-assembly-based chemical gene synthesis: strategies, methods, and progress, Biotechnol. Adv. 26, 121–134.
Czar, M. J., Anderson, J. C., Bader, J. S., and Peccoud, J. (2009) Gene synthesis demystified, Trends. Biotechnol., 27(2):63–72.
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., Merryman, C., Young, L., Noskov, V. N., Glass, J. I., Venter, J. C., Hutchison, C. A., 3rd, and Smith, H. O. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome, Science 319, 1215–1220.
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., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z. Q., Segall-Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison, C. A., 3rd, Smith, H. O., and Venter, J. C. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome, Science 329, 52–56.
Orr-Weaver, T. L., Szostak, J. W., and Rothstein, R. J. (1981) Yeast transformation: a model system for the study of recombination, Proc. Natl. Acad. Sci. USA 78, 6354–6358.
Moerschell, R. P., Tsunasawa, S., and Sherman, F. (1988) Transformation of yeast with synthetic oligonucleotides, Proc. Natl. Acad. Sci. USA 85, 524–528.
Ma, H., Kunes, S., Schatz, P. J., and Botstein, D. (1987) Plasmid construction by homologous recombination in yeast, Gene 58, 201–216.
Raymond, C. K., Sims, E. H., and Olson, M. V. (2002) Linker-mediated recombinational subcloning of large DNA fragments using yeast, Genome Res. 12, 190–197.
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., 3rd. (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.
Gibson, D. G. (2009) Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides, Nucleic Acids Res. 37, 6984–6990.
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.
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the Âsensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res. 22, 4673–4680.
Acknowledgments
The author would like to thank the Synthetic Biology Group at JCVI for the helpful discussions and Synthetic Genomics, Inc. for funding this work.
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Gibson, D.G. (2012). Oligonucleotide Assembly in Yeast to Produce Synthetic DNA Fragments. In: Peccoud, J. (eds) Gene Synthesis. Methods in Molecular Biology, vol 852. Humana Press. https://doi.org/10.1007/978-1-61779-564-0_2
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DOI: https://doi.org/10.1007/978-1-61779-564-0_2
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