Abstract
Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.
Highlights
The synthetic biology toolkit has expanded greatly in recent years, which can be attributed to the efforts of a highly dynamic community of researchers, ambitious undergraduate students in the International Genetically Engineered Machine competition, and the growing number of amateur scientists from the DIY BIO movement
Though as we describe below, PaperClip assembly differentiates itself from Gibson, Circular Polymerase Extension Cloning (CPEC), Seamless Ligation Cloning Extract (SLiCE), and ligase cycling reaction (LCR) assembly methods in that de novo assembly fragments do not need to be generated each time the order assembly is changed (Trubitsyna et al, 2014)
The majority of the rapid prototyping platforms that we have described so far have been optimized for testing biological parts, devices, and systems in vivo; in vitro systems are emerging as a useful testing platform
Summary
The synthetic biology toolkit has expanded greatly in recent years, which can be attributed to the efforts of a highly dynamic community of researchers, ambitious undergraduate students in the International Genetically Engineered Machine competition (iGEM), and the growing number of amateur scientists from the DIY BIO movement. Custom primers are needed to generate inserts de novo each time the assembly order is changed and while it is possible to automate overlap-directed assembly primer design (Hillson et al, 2012), these assembly methods still require tacit knowledge.
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