The Emerging Field of Synthetic Biology: a Review (original) (raw)
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Synthetic biology: applications come of age
NATURE REVIEWS GENETICS, 2010
The circuit-like connectivity of biological parts and their ability to collectively process logical operations was first appreciated nearly 50 years ago 1 . This inspired attempts to describe biological regulation schemes with mathematical models 2-5 and to apply electrical circuit analogies to biological pathways 6,7 . Meanwhile, breakthroughs in genomic research and genetic engineering (for example, recombinant DNA technology) were supplying the inventory and methods necessary to physically construct and assemble biomolecular parts. As a result, synthetic biology was born with the broad goal of engineering or 'wiring' biological circuitry -be it genetic, protein, viral, pathway or genomic -for manifesting logical forms of cellular control. Synthetic biology, equipped with the engineering-driven approaches of modularization, rationalization and modelling, has progressed rapidly and generated an ever-increasing suite of genetic devices and biological modules.
The second wave of synthetic biology: from modules to systems
Nature Reviews Molecular Cell Biology, 2009
Synthetic biology has the potential to transform how we interact with our environment and how we approach human health. Conventional genetic engineering approaches for solving complex problems typically focus on tweaking one or a few genes. Synthetic biology, by contrast, approaches these problems from a novel, engineering-driven perspective that focuses on wholesale changes to existing cellular architectures and the construction of elaborate systems from the ground up. Synthetic biology has the potential to fabricate practical organisms that could clean hazardous waste in inaccessible places 1 , to use plants to sense chemicals and respond accordingly 2,3 , to produce clean fuel in an efficient and sustainable fashion 4 , or to recognize and destroy tumours 5 . Whether addressing an existing problem or creating new capabilities, effective solutions can be inspired by, but need not mimic, natural biological processes. Our new designs can potentially be more robust or efficient than systems that have been fashioned by evolution.
Synthetic biology: new engineering rules for an emerging discipline
MOLECULAR SYSTEMS BIOLOGY, 2006
Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.
The promise of synthetic biology
Applied Microbiology and Biotechnology, 2006
DNA synthesis has become one of the technological bases of a new concept in biology: synthetic biology. The vision of synthetic biology is a systematic, hierarchical design of artificial, biology-inspired systems using robust, standardized, and well-characterized building blocks. The design concept and examples from four fields of application (genetic circuits, protein design, platform technologies, and pathway engineering) are discussed, which demonstrate the usefulness and the promises of synthetic biology. The vision of synthetic biology is to develop complex systems by simplified solutions using available material and knowledge. Synthetic biology also opens a door toward new biomaterials that do not occur in nature.
Asian Journal of Basic Science & Research, 2023
Synthetic biology is an interdisciplinary field that focuses on living organisms and systems, employing engineering techniques to create innovative biological devices, systems, and components. It represents the convergence of old and new approaches, bridging the gap between chemistry and biology, with synthetic chemistry laying the foundation for its emergence. At its core, synthetic biology aims to develop and engineer biological systems by bringing together engineers and biologists to design and construct novel biomolecular parts, circuits, and pathways. These constructs are then utilized to reconstruct, reanalyze, and reprogram organisms for various purposes. There are five primary categories within synthetic biology: bioengineering, synthetic genome, protocell synthetic biology, unconventional molecular biology, and in silico techniques. Traditionally, four engineering approaches have been employed in synthetic biology, including top-down, parallel, orthogonal, and bottom-up methods. These approaches provide a systematic and rational way of reassembling and reconstructing biological components, enabling the creation of functional biological devices, systems, and organisms with known, useful, and novel functions. Synthetic biology holds the promise of providing efficient solutions to various significant challenges in the modern world, encompassing areas such as chemicals, pharmaceuticals, agriculture, energy, and bioremediation. By leveraging engineering methods in the realm of biology, synthetic biology benefits from over 50 years of molecular biological and functional genomic research, along with advanced technologies that allow for the analysis, synthesis, assembly, modification, and transfer of genetic components into living organisms. In essence, synthetic biology offers an exciting avenue to unlock the potential of biological systems and revolutionize multiple industries through innovative modifications and breakthrough innovations.
Synthetic biology - putting engineering into biology
Bioinformatics/computer Applications in The Biosciences, 2006
Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization, and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating, or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis -synthetic biology's system fabrication process -supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.
Developments in the tools and methodologies of synthetic biology
Frontiers in bioengineering and biotechnology, 2014
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 a...
A Perspective of Synthetic Biology: Assembling building blocks for novel functions
Synthetic biology is a recently emerging field that applies engineering formalisms to design and construct new biological parts, devices, and systems for novel functions or life forms that do not exist in nature. Synthetic biology relies on and shares tools from genetic engineering, bioengineering, systems biology and many other engineering disciplines. It is also different from these subjects, in both insights and approach. Applications of synthetic biology have great potential for novel contributions to established fields and for offering opportunities to answer fundamentally new biological questions. This article does not aim at a thorough survey of the literature and detailing progress in all different directions. Instead, it is intended to communicate a way of thinking for synthetic biology in which basic functional elements are defined and assembled into living systems or biomaterials with new properties and behaviors. Four major application areas with a common theme are discussed and a procedure (or “protocol”) for a standard synthetic biology work is suggested.
Synthetic biology by controller design
2022
Natural biological systems display complex regulation and synthetic biomolecular systems have been used to understand their natural counterparts and to parse sophisticated regulations into core design principles. At the same time, the engineering of biomolecular systems has unarguable potential to transform current and to enable new, yet, to be imagined, biotechnology applications. In this review, we discuss the progression of control systems design in synthetic biology, from the purpose of understanding the function of naturally occurring regulatory motifs to that of creating genetic circuits whose function is sufficiently robust for biotechnology applications.