Tying new knots in synthetic biology

Recent years have seen the emergence of synthetic biology, which encompasses the engineering of living organisms as well as the implementation of biological behavior in non‐living substrates. Many of these engineered systems have harnessed the diverse toolkit of proteins, genes, and cellular processes that nature offers. While these efforts have been fruitful, they have also illustrated the difficulty associated with programming highly complex functions by tapping into cellular processes. Another set of efforts has focused on building circuits, performing computation, and constructing nanoscale machines using nucleic acids. Zhang et al., 2007, Science 318, 1121–1125 and Yin etal., 2008, Nature 451, 318–322 recently demonstrated flexible approaches for the modular construction of such biochemical devices exclusively using DNA. These approaches have exciting implications both for engineering living cells and for mimicking life‐like behavior at the nanoscale.

[1]  W. Hess,et al.  Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica. , 2008, Environmental microbiology.

[2]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[3]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[4]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[5]  Ehud Shapiro,et al.  DNA molecule provides a computing machine with both data and fuel , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Ron Weiss,et al.  Genetic circuit building blocks for cellular computation, communications, and signal processing , 2003, Natural Computing.

[7]  E. Winfree,et al.  Construction of an in vitro bistable circuit from synthetic transcriptional switches , 2006, Molecular systems biology.

[8]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[9]  J. Frisvad,et al.  Penicillium svalbardense, a new species from Arctic glacial ice , 2007, Antonie van Leeuwenhoek.

[10]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[11]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[12]  Masami Hagiya,et al.  Computing with Hairpins and Secondary Structures of DNA , 2006, Nanotechnology: Science and Computation.

[13]  L. Excoffier,et al.  Bipolar gene flow in deep‐sea benthic foraminifera , 2007, Molecular ecology.

[14]  Ron Weiss,et al.  Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium , 2007, Proceedings of the National Academy of Sciences.

[15]  Z. Ezziane DNA computing: applications and challenges , 2006 .

[16]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[17]  M. L. Simpson,et al.  Nano-enabled synthetic biology , 2007, Molecular systems biology.

[18]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , .

[19]  C. A. Hutchinson,et al.  Genome transplantation in bacteria: changing one species to another. , 2007, Nature Reviews Microbiology.

[20]  U. Alon,et al.  Negative autoregulation speeds the response times of transcription networks. , 2002, Journal of molecular biology.

[21]  M. L. Simpson,et al.  Gene network shaping of inherent noise spectra , 2006, Nature.

[22]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[23]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[24]  Michael L Simpson,et al.  Cell-free synthetic biology: a bottom-up approach to discovery by design , 2006, Molecular systems biology.

[25]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[26]  S. Lovell,et al.  Protein-protein interaction networks and biology—what's the connection? , 2008, Nature Biotechnology.

[27]  D. Endy Foundations for engineering biology , 2005, Nature.

[28]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[29]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[30]  Gregory D. Peterson,et al.  Engineering in the biological substrate: information processing in genetic circuits , 2004, Proceedings of the IEEE.

[31]  J. Kristjánsson,et al.  Ecology and habitats of extremophiles , 1995, World journal of microbiology & biotechnology.

[32]  J. Doyle,et al.  Bow Ties, Metabolism and Disease , 2022 .

[33]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[34]  T. Weinert,et al.  Toward maintaining the genome: DNA damage and replication checkpoints. , 2002, Annual review of genetics.

[35]  L. Looger,et al.  Computational design of receptor and sensor proteins with novel functions , 2003, Nature.

[36]  A. Turberfield,et al.  DNA fuel for free-running nanomachines. , 2003, Physical review letters.

[37]  J. Macdonald,et al.  Medium scale integration of molecular logic gates in an automaton. , 2006, Nano letters.