Highlights of Research Progress
Synthetic Genome Research
Accurate, Low-Cost Gene Synthesis from Programmable DNA Microchips
Technologies are needed for accurate and cost-effective gene and genome synthesis to support protein production and test the many hypotheses from genomics and systems biology experiments. GTL researchers have developed a microchip-based technology enabling multiplex gene synthesis suitable for large-scale synthetic biology projects. In this approach, pools of thousands of “construction”oligonucleotides (oligos) and tagged complementary “selection”oligos are synthesized on photo-programmable microfluidic chips, released, amplified, and selected by hybridization to reduce synthesis errors ninefold. The oligos then are assembled into multiple genes using a one-step polymerase assembly multiplexing reaction.
These microchips were used to synthesize all the 21 protein-encoding genes making up the Escherichia coli small ribosomal subunit, with translation efficiencies optimized via alteration of codon usage. Researchers estimate that the chip’s synthetic capacity may potentially increase cost-efficiency in oligo yields from 9 bp to 20,000 bp per dollar, depending on the microchip and number of oligos. This technology represents a powerful tool for synthetic biology and complex nanostructures in general. [George Church, Harvard University]
Reference
J. Tian et al., “Accurate Multiplex Gene Synthesis from Programmable DNA Microchips,”Nature 432, 1050–54 [2004].
Generating a Synthetic Genome
Researchers at the Institute for Biological Energy Alternatives (IBEA, now called the J. Craig Venter Institute) have advanced methods to improve the speed and accuracy of genomic synthesis. The team assembled the 5386-bp bacteriophage φX174 (phi X), using short, single strands of synthetically produced, commercially available DNA (oligonucleotides). Researchers employed an adaptation of the polymerase chain reaction (PCR) known as polymerase cycle assembly (PCA) to build the phi X genome. Like PCR, PCA is a technique that produces double-stranded copies of individual gene sequences based on single-stranded templates. IBEA assembled the synthetic phi X in just 14 days.
Reference
H. O. Smith et al., “Generating a Synthetic Genome by Whole Genome Assembly: φX174 Bacteriophage from Synthetic Oligonucleotides,”Proc. Natl. Acad. Sci. 100(26), 15440–445 (2003).
