Synthetic genomes: The next step for the synthetic genome

@article{Baker2011SyntheticGT,
  title={Synthetic genomes: The next step for the synthetic genome},
  author={Monya Baker},
  journal={Nature},
  year={2011},
  volume={473},
  pages={403-408}
}
  • M. Baker
  • Published 1 May 2011
  • Biology
  • Nature
Biologists have copied an existing genetic code, but haven't yet commercialized it or written their own. What will it take for a tour de force to reach industrial force? 

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References

SHOWING 1-10 OF 13 REFERENCES

Chemical synthesis of the mouse mitochondrial genome

TLDR
A one-step, isothermal assembly method for synthesizing DNA molecules from overlapping oligonucleotides that synthesizes the entire 16.3-kilobase mouse mitochondrial genome from 600 overlapping 60-mers is described.

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

TLDR
The design, synthesis, and assembly of the 1.08–mega–base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new cells that are controlled only by the synthetic chromosome are reported.

Enzymatic assembly of DNA molecules up to several hundred kilobases

We describe an isothermal, single-reaction method for assembling multiple overlapping DNA molecules by the concerted action of a 5′ exonuclease, a DNA polymerase and a DNA ligase. First we recessed

One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome

TLDR
Assembly of the synthetic genome from 25 overlapping fragments in a single step using yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments.

DNA assembly for synthetic biology: from parts to pathways and beyond.

TLDR
This review provides a critical examination of recent DNA assembly strategies and considers how this important facilitating aspect of synthetic biology may proceed in the future.

A brief review of DNA and RNA chemical synthesis.

  • M. Caruthers
  • Chemistry, Biology
    Biochemical Society transactions
  • 2011
Current methodologies used to synthesize DNA and RNA are reviewed. These focus on using controlled pore glass and microarrays on glass slides.

Programming cells by multiplex genome engineering and accelerated evolution

TLDR
The multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties by facilitating rapid and continuous generation of a diverse set of genetic changes.

Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome.

TLDR
Given the significant diversity in genome structure observed upon horizontal DNA transfer in nature, this stable laboratory-generated composite genome raised fundamental questions concerning two complete genomes in one cell and may be generally applicable to other genomes or genome loci of free-living organisms.

Parallel on-chip gene synthesis and application to optimization of protein expression

TLDR
An on-chip gene synthesis technology, which integrates on a single microchip the synthesis of DNA oligonucleotides using inkjet printing, isothermal oligon nucleotide amplification and parallel gene assembly, which may facilitate systematic investigation of the molecular mechanisms of protein translation and the design, construction and evolution of macromolecular machines, metabolic networks and synthetic cells.

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

TLDR
This work uses high-fidelity DNA microchips, selective oligonucleotide pool amplification, optimized gene assembly protocols and enzymatic error correction to develop a method for highly parallel gene synthesis.