Bringing next-generation therapeutics to the clinic through synthetic biology

Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
Current opinion in chemical biology (Impact Factor: 6.81). 05/2012; 16(3-4):355-61. DOI: 10.1016/j.cbpa.2012.04.009
Source: PubMed


Recent advances in synthetic biology have created genetic tools with the potential to enhance the specificity, dynamic control, efficacy, and safety of medical treatments. Interfacing these genetic devices with human patients may thus bring about more efficient treatments or entirely new solutions to presently intractable maladies. Here we review engineered circuits with clinical potential and discuss their design, implementation, and validation.

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    • "Synthetic bacterial pathways and circuits are of great interest for the production of industrial chemicals (1–3) and biofuels (4–7), as well as for biosensing (8,9) and biomedical purposes (10–14). A major goal of synthetic biology is to facilitate these efforts by enabling the assembly of multigene circuits in which each part performs its function predictably, while minimizing unexpected interactions between parts (15,16). "
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    ABSTRACT: In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.
    Nucleic Acids Research 09/2013; 42(1). DOI:10.1093/nar/gkt860 · 9.11 Impact Factor
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    • "A major focus of synthetic biology is the design of genetic circuits that program cellular functions in living organisms. The development of such circuits in mammalian cells has the potential to lead to new strategies for cell-based therapies and diagnostics (1–3). Bio-molecular computing systems have been implemented using various components, including recombinases, small RNAs, riboswitches and natural and artificial transcription factors (TFs) (4). "
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    ABSTRACT: Biological computing circuits can enhance our ability to control cellular functions and have potential applications in tissue engineering and medical treatments. Transcriptional activator-like effectors (TALEs) represent attractive components of synthetic gene regulatory circuits, as they can be designed de novo to target a given DNA sequence. We here demonstrate that TALEs can perform Boolean logic computation in mammalian cells. Using a split-intein protein-splicing strategy, we show that a functional TALE can be reconstituted from two inactive parts, thus generating two-input AND logic computation. We further demonstrate three-piece intein splicing in mammalian cells and use it to perform three-input AND computation. Using methods for random as well as targeted insertion of these relatively large genetic circuits, we show that TALE-based logic circuits are functional when integrated into the genome of mouse embryonic stem cells. Comparing construct variants in the same genomic context, we modulated the strength of the TALE-responsive promoter to improve the output of these circuits. Our work establishes split TALEs as a tool for building logic computation with the potential of controlling expression of endogenous genes or transgenes in response to a combination of cellular signals.
    Nucleic Acids Research 08/2013; 41(21). DOI:10.1093/nar/gkt758 · 9.11 Impact Factor
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    ABSTRACT: Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.
    Nature Protocols 09/2014; 9(9):2075-2089. DOI:10.1038/nprot.2014.145 · 9.67 Impact Factor
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