A survey of enabling technologies in synthetic biology

Abstract

BackgroundRealizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies.ResultsWe conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants.ConclusionsThe set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential.

Bricks and blueprints: methods and standards for DNA assembly

“…Golden Gate assembly is at the heart of many of the kits for genome-editing (Box 1), so numerous labs will already be familiar with its ability to assemble many different parts in a defined order in a single reaction. Likewise, Gibson assembly has become the method of choice in synthetic biology 60 and has even been used to assemble an entire mouse mitochondrial genome from hundreds of oligonucleotides 61 . Implementing standards for large DNA assembly projects is also beginning to bear fruit.…”

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

“…The outreach efforts of the SBOL Developers Group have helped to attract early adopters. Recently, 18% of self-identified synthetic biologists responding to a survey reported current use of SBOL and 10% past use 15 , the highest use among standards and methods for measurement, functional composition and data exchange in the survey. This base level of support forms a foundation for broader community adoption.…”

A parity check analog decoder for molecular communication based on biological circuits

“…At the same time, the considerations made for the Hill function in Section VI-A can be extended to the complementary Hill function. Again, using the same notation as in (6), for K p = 1 and n = 2, we obtain…”

“…U 2 and U 3 have concentration values L(y 2 |x 2 ) and L(y 3 |x 3 ), respectively. Both these Gene Expression Circuits give as output (operons) the molecules A 0 , T 0 , D 0 whose concentrations are related to the input through the Hill function in (6).…”

“…Recent advances in synthetic biology are providing new tools for the design, realization, and control of biological processes through the programming of cells' genetic code [6]. In particular, the theory of biological circuits, based on networks of DNA genes linked together by activation and repression mechanisms that regulate their expression into proteins, provides basic components and processes to design functionalities and behaviors in cells, mostly bacteria, by following an engineering-based approach [7], [8].…”