Synthetic biology

  • Article |

    A modular de novo designed biosensor platform consisting of a cage and key molecule is developed, and used to create sensors for seven distinct proteins including the spike protein from SARS-CoV-2 and anti-SARS antibodies.

    • Alfredo Quijano-Rubio
    • , Hsien-Wei Yeh
    •  & David Baker
  • Article |

    A technique for the de novo design of switchable protein systems controlled by induced conformational change is demonstrated for three functional motifs, in vitro and in yeast and mammalian cells.

    • Robert A. Langan
    • , Scott E. Boyken
    •  & David Baker
  • Article |

    High-fidelity convergent total synthesis is used to produce Escherichia coli with a 61-codon synthetic genome that uses 59 codons to encode all of the canonical amino acids.

    • Julius Fredens
    • , Kaihang Wang
    •  & Jason W. Chin
  • Article |

    An RNA-adapting CRISPR–Cas system is coupled with amplification and sequencing steps to record, retrieve and analyse changes in the transcriptome of a bacterial cell over time.

    • Florian Schmidt
    • , Mariia Y. Cherepkova
    •  & Randall J. Platt
  • Letter |

    Computationally designed icosahedral protein-based assemblies can protect their genetic material and evolve in biochemical environments, suggesting a route to the custom design of synthetic nanomaterials for non-viral drug delivery.

    • Gabriel L. Butterfield
    • , Marc J. Lajoie
    •  & David Baker
  • Letter |

    A genetically encoded platform can produce chiral organoboranes in bacteria with high turnover, enantioselectivity and chemoselectivity, and can be tuned and configured through DNA manipulation.

    • S. B. Jennifer Kan
    • , Xiongyi Huang
    •  & Frances H. Arnold
  • Review Article |

    A review of the recent developments in reprogramming the genetic code of cells and organisms to include non-canonical amino acids in precisely engineered proteins.

    • Jason W. Chin
  • Letter |

    The class 2 type VI RNA-guided RNA-targeting CRISPR–Cas effector Cas13 can be engineered for RNA knockdown and binding, expanding the CRISPR toolset with a flexible platform for studying RNA in mammalian cells and therapeutic development.

    • Omar O. Abudayyeh
    • , Jonathan S. Gootenberg
    •  & Feng Zhang
  • Letter |

    The first synthetic genetic oscillator or ‘repressilator’ is simplified using insights from stochastic theory, thus achieving remarkably precise and robust oscillations and informing current debates about the next generation of synthetic circuits and their potential applications in cell-based therapies.

    • Laurent Potvin-Trottier
    • , Nathan D. Lord
    •  & Johan Paulsson
  • Letter |

    Clinically relevant bacteria have been engineered to lyse synchronously at a threshold population density and release genetically encoded therapeutics; treatment of mice with these bacteria slowed the growth of tumours.

    • M. Omar Din
    • , Tal Danino
    •  & Jeff Hasty
  • Letter |

    A ribosome with tethered subunits, ‘Ribo-T’, is engineered by making a hybrid RNA composed of ribosomal RNA of large and small subunits; Ribo-T can support cell growth in vivo in the absence of wild-type ribosomes, and is used to establish a fully orthogonal ribosome–mRNA system.

    • Cédric Orelle
    • , Erik D. Carlson
    •  & Alexander S. Mankin
  • Letter |

    Triphosphates of hydrophobic nucleotides d5SICS and dNaM are imported into Escherichia coli by an exogenous algal nucleotide triphosphate transporter and then used by an endogenous polymerase to replicate, and faithfully maintain over many generations of growth, a plasmid containing the d5SICS–dNaM unnatural base pair.

    • Denis A. Malyshev
    • , Kirandeep Dhami
    •  & Floyd E. Romesberg
  • Letter |

    Protease competition is used to produce rapid and tunable coupling of genetic circuits, enabling a coupled clock network that can encode independent environmental cues into a single time series output, a form of frequency multiplexing in a genetic circuit context.

    • Arthur Prindle
    • , Jangir Selimkhanov
    •  & Jeff Hasty
  • Letter |

    Synthetic analog gene circuits can be engineered to execute logarithmically linear sensing, addition, ratiometric and power-law computations in living cells using just three transcription factors.

    • Ramiz Daniel
    • , Jacob R. Rubens
    •  & Timothy K. Lu
  • Letter |

    Saccharomyces cerevisiae is engineered to produce high concentrations of artemisinic acid, a precursor of the artemisinin used in combination therapies for malaria treatment; an efficient and practical chemical process to convert artemisinic acid to artemisinin is also developed.

    • C. J. Paddon
    • , P. J. Westfall
    •  & J. D. Newman
  • Letter |

    An efficient and scalable strategy with robust error correction is reported for encoding a record amount of information (including images, text and audio files) in DNA strands; a ‘DNA archive’ has been synthesized, shipped from the USA to Germany, sequenced and the information read.

    • Nick Goldman
    • , Paul Bertone
    •  & Ewan Birney
  • Letter |

    A bilayer material comprising catalyst-bearing microstructures embedded in a responsive gel and actuated into and out of a reactant-containing ‘nutrient’ layer continuously interconverts chemical, thermal and mechanical energy and thereby shows autonomous, self-sustained homeostatic behaviour, which regulates the temperature of the system in a narrow range.

    • Ximin He
    • , Michael Aizenberg
    •  & Joanna Aizenberg
  • Letter |

    In synthetic biology, the use of regulatory proteins that bind either DNA or RNA to reprogram mammalian cellular functions allows a variety of computational ‘logic circuits’ to be built in a plug-and-play manner, which may pave the way for precise and robust control of future gene-based and cell-based therapies.

    • Simon Ausländer
    • , David Ausländer
    •  & Martin Fussenegger
  • Article |

    Thousands of quorum-sensing Escherichia coli colonies are synchronized over centimetres using redox signalling to create ‘biopixels’ that can sense trace amounts of arsenic in water.

    • Arthur Prindle
    • , Phillip Samayoa
    •  & Jeff Hasty
  • Letter |

    Although new amino acids with desirable properties can be devised, only a few have been successfully introduced into proteins by the cellular machinery. Even then, only one type of unnatural amino acid can be added to a given protein. Here, a new system has been designed that could allow the incorporation of up to 200 novel amino acids. The system involves an orthogonal ribosome that uses quadruplet — rather than triplet — codons, as well as orthogonal tRNA synthetase–tRNA pairs.

    • Heinz Neumann
    • , Kaihang Wang
    •  & Jason W. Chin
  • Article |

    A defining focus of synthetic biology is the engineering of genetic circuits with predictive functionality in living cells. Here, a decade after the first synthesized genetic toggle switch and oscillator, an engineered gene network with global intercellular coupling is designed that is capable of generating synchronized oscillations in a growing population of cells.

    • Tal Danino
    • , Octavio Mondragón-Palomino
    •  & Jeff Hasty