Since the launch of the Human Genome Project, the genomes of over 180 organisms have been sequenced. While this information is extremely valuable, researchers must leverage this data into actionable applications. Synthetic biology, which applies engineering principles to the design of biological systems, has the potential to utilize sequencing information and innovate in such diverse areas as biomaterials, industrial enzymes, pest-resistant crops and personalized medicine. However, the capacity to synthesize DNA significantly lags behind the ability to sequence it. Currently, about 3000 times more DNA is sequenced than synthesized, a conundrum often referred to as the “read-write gap.”
Closing the read-write gap
Significant innovation in synthesizing DNA is required to close this read-write gap. To do this, new methods must be developed to address old issues that hinder the scalability of DNA synthesis. For example, traditional synthesis of gene-length DNA constructs starts with the production of individual oligonucleotides (oligos), followed by assembly into longer-length constructs. Producing oligonucleotides in parallel by hundreds of thousands (several orders of magnitude higher than current methods) is necessary to increase the throughput of gene assembly. Further, methods to improve fidelity must be employed to overcome inherent errors that occur during oligonucleotide synthesis and assembly stages. Advances in these areas will enable DNA synthesis to reach the Moore’s law-like exponential growth witnessed in DNA sequencing.
Scaling gene synthesis with multiplex technology
Figure 1 – Gen9’s BioFab platform allows for massively parallel, high-throughput DNA construction.Traditional solutions to scale DNA synthesis capacity include linear addition of equipment and labor. However, this solution is costly in the long term. Other more promising options include microfluidics (miniaturization to drive volume reductions) and multiplexing (building many things at one time). The BioFab platform from Gen9 (Cambridge, Mass.) employs multiple technologies to build a highly scalable manufacturing process for synthetic DNA (see Figure 1).
The BioFab platform is the first industrialized, chip-based manufacturing technology for gene synthesis and assembly. The process begins with an ordering portal that enables scientists to easily and efficiently upload and design multiple DNA sequences at one time. Sophisticated design algorithms then parse each DNA construct into oligonucleotide-length fragments, creating optimal conditions for synthesis. Hundreds of thousands of oligos are then chemically synthesized on high-density microarray chips. Eventually, longer DNA constructs are assembled from these oligos using a high-throughput assembly process. Given the number of oligos, fragments and constructs processed using the platform, it is essential to have an informatics infrastructure for scaling gene synthesis. The BioFab execution system automates and intelligently guides DNA synthesis, allows longer and more complicated sequences and is coupled to cloud-based tools that enable data-mining and metrics-tracking from DNA design to manufacture to shipment. In addition to the informatics systems, unique error-correction strategies are used during the assembly process for efficient, high-throughput construction of DNA, up to 10,000 base pairs in length. Finally, next-generation sequencing confirms accuracy of the final synthetic DNA construct.
Early studies show that 50 individual DNA synthesis reactions can be multiplexed in a single well (Figure 2), and it is projected that this will scale DNA manufacturing, leading to the ability to synthesize 1 billion base pairs of DNA—the current annual global demand for DNA—in just one month. Moreover, the platform’s increased capacity will lower costs by reducing reagent waste and maximizing DNA assembly.
Figure 2 – Early studies show that 50 individual DNA synthesis reactions can be multiplexed in a single well.Scaling gene synthesis
The ability to synthesize billions of DNA base pairs will drive a number of applications. For example, researchers are already exploring the possibility of using DNA as a storage medium. DNA is one of the oldest and most robust information storage methods on the planet. Recent experiments show that it can be used to house multiple types of data (such as text, photos and music). Unlike digital storage, however, DNA can survive for tens of thousands of years with a minimal physical footprint and low energy consumption. At a time when more information content is produced than ever before, DNA data storage is an attractive alternative.
The use of DNA for information storage has been demonstrated by one of Gen9’s founders, George Church, who recently encoded a book into DNA. He showed that in a space smaller than a thumb drive, 70 billion unique books could be encoded. The technology to store any information in the form of DNA is primarily limited only by synthesis capacity and cost; multiplexed DNA synthesis can help remove these barriers.
Devin Leake is vice president of research and development, Gen9, Inc., 840 Memorial Dr., Cambridge, Mass. 02139, U.S.A.; tel.: 617-250-8433; e-mail: [email protected]; www.gen9bio.com