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Applying Moore's Law to DNA Synthesis
Next-generation gene synthesis could be as transformative for several multibillion-dollar industries as the semiconductor.!--h2>
Over the past 60 years researchers have spent a great deal of time and money devoted to the reading and interpreting of DNA. But despite the many improvements in our ability to read this code with ever accelerating speed and accuracy, our ability to write it—assemble a desired sequence and synthesize it into DNA—has remained rudimentary at best. The field of synthetic biology is devoted to the writing of DNA. For the full potential of this field to be realized, there need to be dramatic advances in the accuracy, reliability, cost, and turnaround time of writing DNA if it is ever to catch up with and exploit the discoveries being made as a result of our ever-increasing ability to read it.
For such a tremendously important molecule, this limitation is a serious handicap. As DNA sequencing makes strides faster than ever, our next step will naturally be to predict biological changes, perhaps in proteins or RNA, and we are missing a fundamental piece of the puzzle if we cannot go back and specifically write the predicted section of DNA to make that altered protein or RNA. At Gen9, we have developed a gene synthesis fabrication capability that derives from the work of three leaders in fields of microelectronics, bioengineering, and genetics: Joseph Jacobson (Massachusetts Institute of Technology, MIT), Drew Endy (Stanford University), and George Church (Harvard University). This technology platform offers a next-generation approach to gene synthesis and is the first major leap forward in writing DNA faster, better, and cheaper that the field has seen in years.
The Gen9 platform is more than just a technical accomplishment. The current limitations in manufacturing synthetic DNA have hobbled its growth as an engineering tool for many industrial applications in fields that could otherwise see real improvements from its use. With better, more cost-effective, and scalable DNA synthesis, industries ranging from agricultural biotechnology and enzyme manufacturing to biofuels and specialty chemicals stand to make rapid and significant gains. Next-generation gene synthesis could prove to be as transformative for these and other multibillion-dollar industries as has been the semiconductor.
DNA Synthesis: A Synopsis
Oligonucleotide synthesis is the most common method of building desired DNA sequences. The techniques for doing this were conceived as early as the 1950s in the laboratory of Alexander Todd, a Scottish biochemist who would go on to win the Nobel Prize in Chemistry. Within 30 years, the method had become so reliable that it was automated and used in laboratories around the world.
Eventually, oligo synthesis became so automated and routine that it no longer made sense for each lab to build its own oligos. Instead, core laboratories, and eventually commercial manufacturers, became the primary source for increasingly accurate and lower-cost oligos. Today, these industrial-scale facilities churn out built-to-order DNA sequences in large volumes. Still, oligo synthesis has its limitations. The longer an oligo construct, the higher the rate of base composition errors in fabricating the construct. To ensure accuracy, oligos are usually kept to 200 base pairs or shorter. Advances have been made in assembling these 200-base oligos together to build much longer constructs. However, errors can accumulate in the assembly process, and the labor required in piecing together these longer constructs means they are costly and time-intensive to produce. Another drawback of this approach is that it is not scalable; the doubling of capacity requires a doubling of resources and overhead.
Recently, scientists at Harvard, MIT, and Stanford used synthetic biology as the platform for a completely novel approach to building DNA constructs which, due to its ability to provide large libraries of genes at costs substantially lower than what is available today, can provide a beneficial disruption to the field of synthetic biology. This technology—built by Endy, Church, and Jacobson—became the foundation for Gen9.
Key elements of the technology that differentiate it from other gene synthesis approaches are its highly multiplexed nature and error-correction method. Originally made on adapted microarrays, the founders' technology enabled the building of millions of oligos in parallel—unlike the much slower serial techniques used by other platforms. An error-correction protocol in which engineered proteins are deployed to detect and eliminate mistakes makes it possible to manufacture far longer stretches of DNA without base errors.
Building on these concepts, Gen9 developed the first technology to synthesize genes from silicon chips and used it to build a novel, massive-scale fabrication plant for synthetic DNA. Known as the BioFab® platform, this technology has the capacity to generate tens of thousands of synthetic gene fragments per year in just a few dozen square feet of laboratory space. Because of the nature of the Gen9 technology, capacity can be ramped up on a logarithmic, rather than linear, scale.
This ability to scale exponentially means that we can finally operate within Moore's Law—the trend in computer manufacturing that has successfully doubled capacity approximately every 2 years over many decades. That relentless pace, which has become a standard for any kind of meaningful industrial progress over the long-term, is now achievable in gene synthesis. A manufacturing process that can promise dramatic improvements in quality and capacity while continually offering lower pricing has the ability to transform how synthetic biology is practiced.
Today, Gen9 is manufacturing and shipping double-stranded gene fragments from 500 to 1,024 base pairs called GeneBits™ constructs. Each GeneBits construct has error rates better than 1:2,500 as linear DNA and is confirmed with consensus sequencing. The company is continually working to improve both construct length and accuracy, and in early 2013 expects to commercialize both GeneBits Perfects and GeneBytes constructs up to 3 Kbp to address another area of unmet need in the marketplace. This will extend the ability of customers to focus not on the production of their needed genes but instead on new applications and opportunities of synthetic biology.
Capacity, Accuracy, and Cost
Gen9's innovation in gene synthesis enables significantly higher capacity, improved fidelity compared to other approaches, and, most importantly, dramatically lower costs. Taken together, these three advantages will enable expanded use of DNA constructs in industries and applications that had not previously considered them a real possibility before because of cost and availability barriers.
By the end of 2012, Gen9 had the technology and capacity to produce approximately 50% of the world's current supply of synthetic DNA. We estimate that sometime in 2013 technological improvements to the BioFab platform will enable us to double the global capacity of synthetic DNA production. With that kind of rapid increase, there will be enough reliable synthetic DNA to make this an interesting, and eventually indispensable, source of experimental tools across a range of industries.
As the length of constructs increases, the issue of accuracy becomes a larger concern. Until now, it has been a major sticking point in producing longer DNA constructs. The Gen9 platform is the first commercial technology that will enable the production of long, error-free stretches of DNA in large volumes and at affordable prices. With high-accuracy constructs in the multiple-Kbp range, scientists in biology and many other industrial fields will be able to study the behavior of full genes, metabolic pathways, distant genetic elements, genomes, and new aspects of DNA that cannot currently be interrogated, or even created, with synthetic constructs.
The current average cost for an oligo construct is close to 40 cents per base. That number has slowly come down over the last few years but, without a major technological leap, it probably will not change measurably in the coming years. This price of 40 cents, while a vast improvement over what people had to pay for oligos 10 or 15 years ago, is still prohibitive for scientists who want to use gene constructs in a high-throughput manner. In addition, when the size of the desired constructs becomes multiple Kbp, this price soars to the dollars-per-base pair range. While the current price may be acceptable for academic biology labs that use only a handful of gene constructs at a time, it is a deal-breaker for the industrial-scale screening processes implemented at major corporations that could otherwise make use of synthetic DNA. Because the Gen9 platform can scale in an exponential way, we anticipate being able to drive costs even lower as we ramp up production.
Just as improved DNA sequencing enabled a shift in focus from studying individual genes to examining a whole genome or multiple genomes at once, this improvement in gene synthesis foreshadows much the same shift in synthetic biology. As costs come down, scientists will be able to move from synthesizing individual genes to whole pathways or even full genomes. For example, the first known synthetic genome was produced by Craig Venter and a team of researchers at a cost of $40 million. Bringing that price tag down exponentially in the coming years will make these types of synthetic biology projects far more feasible in industry and academia.
With next-generation gene synthesis, DNA can finally offer commercial industry a source of biologically derived building blocks. Consider the transformation of the chemistry industry in the 20th century as monomers and polymers became standard ingredients for any number of newly created materials, such as nylons, plastics, and Kevlar. Scientists and engineers were able to create whole new fabrics and other materials by screening possible combinations of monomers and polymers and testing and tweaking their designs to make the materials meet various criteria—all thanks to having access to inexpensive chemical building blocks that could be mixed and screened in a massively parallel way. We believe that DNA will be to the 21st century what polymers were to the 20th. With access to highly accurate, low-cost synthetic genes, any number of industries will be able to perform high-throughput screening to determine which genetic code makes for the most efficient enzyme, the most robust crop strain, or anything else they might imagine.
The first industries to adopt synthetic DNA—and several already have a toe in the water—will be manufacturers of enzymes, biofuels, and agricultural biotechnology products. These early adopters include Dow Chemicals, DuPont (the parent company of Genencor and Pioneer Hybrid), Sapphire Energy, and Monsanto, among many others. As we attempt to wean ourselves from oil dependency, for instance, enzyme design companies will be able to test various gene constructs to determine which new enzymes might best represent an alternative to those used in petroleum-based products. Companies striving to design biofuels are already using DNA constructs to screen for pathways that optimize energy production and other components; their success hinges on access to low-cost, high-throughput synthetic DNA. Biosynthesis allows for manufacturing with renewable feedstocks at much higher volume and lower cost than industrial processes that currently rely on fossil fuels. It also gives companies the ability to create materials (including nano-inorganic products) that cannot be synthesized chemically in the lab, opening the doors for completely new possibilities in material engineering.
Today, the global market for chemicals that could be “biosynthesized” is an estimated $50 billion, and $500 billion for biofuels. If you consider the potential for synthetic genes to revolutionize these and many other industries, we think the opportunity is virtually limitless. With that in mind, it is clear that next-generation gene synthesis stands to be as transformative in the years to come as the semiconductor chip has been in the past several decades.
Indeed, synthetic DNA has already shown promise in one industry that may not be intuitively linked to it: information storage. One of our co-founders, George Church, recently demonstrated that it was possible to convert all of the information in a book and to write that information in DNA. An entire book—about 700 terabytes of data—was stored in a single gram of DNA, using the biological molecule's A, C, T, and G to stand in for the typical zeros and ones of computer binary language. When the achievement was published, Church was quoted as saying that with DNA-based storage for computers, “a device the size of your thumb could store as much information as the whole internet.” This points to a coming revolution in electronics as the use of synthetic DNA takes off.
As with any technology, there is the potential for misuse and harm. The constructive use of the advances in synthetic DNA must be a priority for everyone. The World Health Organization and governmental agencies such as the National Institutes of Health, the Centers for Disease Control and Prevention, and the European Biosafety Association have all issued guidelines and laws to help protect against misuse. Organizations such as Internationally Genetically Engineerined Machine have also made safety and security a priority for their programs.
As a manufacturer of synthetic DNA constructs, Gen9 follows the Screening Framework Guidance issued by the US government for Providers of Synthetic Double-Stranded DNA. This framework describes how commercial providers of synthetic genes should perform gene sequence and customer screening. As an applicant member organization we also recognize and abide by the Harmonized Screening Protocol of the International Gene Synthesis Consortium (IGSC). The Harmonized Screening Protocol describes the gene sequence and customer screening practices that IGSC member companies employ to prevent the misuse of synthetic genes. For example, we screen all orders against a government-maintained watchlist to ensure that customers are not ordering DNA that could be used to build a known pathogen.
By the mid-1900s, chemical engineering had ushered in a wave of innovation that used synthesized polymers to introduce all sorts of new materials into general use. Plastic is just one of many examples; it is hard to make it through the day without using a product that has benefited from chemical engineering. In the last several decades, we have seen a similar revolution based on the semiconductor chip and the countless advances it has enabled in far-flung industries. From cars to phones to household appliances, these chips have completely changed the way we interact with consumer tools.
We believe that the next big frontier in innovation will be led by biological engineering, as high-accuracy, low-cost synthetic DNA allows entire industries to experiment in ways they never could before. Research teams will be able to predict DNA sequences and test their functions faster and more reliably than ever, and that testing will support the development of new materials, optimized enzymes, higher-efficiency biofuels, and much more.
Industrial Biotechnology, published by Mary Ann Liebert, Inc., is a peer-reviewed bimonthly research journal focused on biobased industrial and environmental products and processes. The above article was first published in the February 2013 issue of Industrial Biotechnology with the title “BioFab: Applying Moore’s Law to DNA Synthesis”. The views expressed here are those of the authors and are not necessarily those of Industrial Biotechnology journal, Mary Ann Liebert, Inc., publishers, or their affiliates. No endorsement of any entity or technology is implied.
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