DNA-based Communication in Populations of Synthetic Protocells

Developing molecular communication platforms based on orthogonal communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled ‘biomolecular implementation of protocellular communication’ (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.Semipermeable proteinosome membranes allow complex DNA message communication through compartmentalization and protect the DNA circuits from degradation in a biological environment.

[1]  B. Bassler,et al.  Quorum sensing: cell-to-cell communication in bacteria. , 2005, Annual review of cell and developmental biology.

[2]  Lulu Qian,et al.  Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks , 2018, Nature.

[3]  Erik Winfree,et al.  Enzyme-free nucleic acid dynamical systems , 2017, Science.

[4]  Mat E. Barnet,et al.  A synthetic Escherichia coli predator–prey ecosystem , 2008, Molecular systems biology.

[5]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[6]  A S Verkman,et al.  Size-dependent DNA Mobility in Cytoplasm and Nucleus* , 2000, The Journal of Biological Chemistry.

[7]  Georg Seelig,et al.  Computational Design of Reaction-Diffusion Patterns Using DNA-Based Chemical Reaction Networks , 2014, DNA.

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

[9]  Luca Cardelli,et al.  Programmable chemical controllers made from DNA. , 2013, Nature nanotechnology.

[10]  Friedrich C Simmel,et al.  Robustness of localized DNA strand displacement cascades. , 2014, ACS nano.

[11]  G. Seelig,et al.  Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.

[12]  Katherine E. Dunn,et al.  Investigating the dynamics of surface-immobilized DNA nanomachines , 2016, Scientific Reports.

[13]  Oscar Ces,et al.  Artificial cell mimics as simplified models for the study of cell biology , 2017, Experimental biology and medicine.

[14]  Stephen Mann,et al.  Chemical Signaling and Functional Activation in Colloidosome-Based Protocells. , 2016, Small.

[15]  Jie Chao,et al.  Clamped Hybridization Chain Reactions for the Self-Assembly of Patterned DNA Hydrogels. , 2017, Angewandte Chemie.

[16]  M. Freeman.  Feedback control of intercellular signalling in development , 2000, Nature.

[17]  Lingchong You,et al.  Coupling spatial segregation with synthetic circuits to control bacterial survival , 2016, Molecular systems biology.

[18]  F T Vertosick,et al.  Immune network theory: a role for parallel distributed processing? , 1989, Immunology.

[19]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[20]  Stephen Mann,et al.  Predatory behaviour in synthetic protocell communities. , 2017, Nature chemistry.

[21]  M. Isalan,et al.  Sender–receiver systems and applying information theory for quantitative synthetic biology , 2015, Current opinion in biotechnology.

[22]  Xi Chen,et al.  Stacking nonenzymatic circuits for high signal gain , 2013, Proceedings of the National Academy of Sciences.

[23]  Edward S Boyden,et al.  Engineering genetic circuit interactions within and between synthetic minimal cells , 2016, Nature chemistry.

[24]  Xin Huang,et al.  Construction of biological hybrid microcapsules with defined permeability towards programmed release of biomacromolecules. , 2017, Chemical communications.

[25]  Andrew J. deMello,et al.  Microfluidic formation of proteinosomes. , 2018, Chemical communications.

[26]  Georg Seelig,et al.  A spatially localized architecture for fast and modular DNA computing. , 2017, Nature nanotechnology.

[27]  Georg Seelig,et al.  A molecular multi-gene classifier for disease diagnostics , 2018, Nature Chemistry.

[28]  Javier Macía,et al.  Distributed biological computation with multicellular engineered networks , 2011, Nature.

[29]  Stephen Mann,et al.  Gene-Mediated Chemical Communication in Synthetic Protocell Communities. , 2017, ACS synthetic biology.

[30]  Wendell A Lim,et al.  Design principles of regulatory networks: searching for the molecular algorithms of the cell. , 2013, Molecular cell.

[31]  Milan N Stojanovic,et al.  Networking particles over distance using oligonucleotide-based devices. , 2007, Journal of the American Chemical Society.

[32]  S. Mansy,et al.  Communicating artificial cells. , 2016, Current opinion in chemical biology.

[33]  Jonathan Grizou,et al.  Artificial intelligence exploration of unstable protocells leads to predictable properties and discovery of collective behavior , 2018, Proceedings of the National Academy of Sciences.

[34]  G Gines,et al.  Microscopic agents programmed by DNA circuits. , 2017, Nature nanotechnology.

[35]  Drew Endy,et al.  Engineered cell-cell communication via DNA messaging , 2012, Journal of biological engineering.

[36]  Stephen Mann,et al.  Interfacial assembly of protein–polymer nano-conjugates into stimulus-responsive biomimetic protocells , 2013, Nature Communications.

[37]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[38]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[39]  Matthew R. Lakin,et al.  Bioinformatics Applications Note Systems Biology Visual Dsd: a Design and Analysis Tool for Dna Strand Displacement Systems , 2022 .

[40]  Conrad Steenberg,et al.  NUPACK: Analysis and design of nucleic acid systems , 2011, J. Comput. Chem..

[41]  Dominic Scalise,et al.  DNA Strand-Displacement Timer Circuits. , 2017, ACS synthetic biology.

[42]  Rebecca Schulman,et al.  Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium. , 2017, ACS synthetic biology.

[43]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[44]  Yaron E. Antebi,et al.  Design principles of cell circuits with paradoxical components , 2012, Proceedings of the National Academy of Sciences.

[45]  Christopher A. Voigt,et al.  Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.

[46]  Christopher A. Voigt,et al.  A Synthetic Genetic Edge Detection Program , 2009, Cell.

[47]  Martin Fussenegger,et al.  Synthetic two-way communication between mammalian cells , 2012, Nature Biotechnology.

[48]  Bastiaan C. Buddingh,et al.  Artificial Cells: Synthetic Compartments with Life-like Functionality and Adaptivity , 2017, Accounts of chemical research.

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

[50]  Teruo Fujii,et al.  Quencher-free multiplexed monitoring of DNA reaction circuits , 2012, Nucleic acids research.

[51]  Wendell A. Lim,et al.  Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors , 2014, Science.

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

[53]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[54]  Richard A. Muscat,et al.  DNA nanotechnology from the test tube to the cell. , 2015, Nature nanotechnology.

[55]  Brian M. Frezza,et al.  Modular multi-level circuits from immobilized DNA-based logic gates. , 2007, Journal of the American Chemical Society.

[56]  Hyun Youk,et al.  Autocrine Signaling and Quorum Sensing: Extreme Ends of a Common Spectrum. , 2016, Trends in cell biology.

[57]  S. Quake,et al.  Monolithic microfabricated valves and pumps by multilayer soft lithography. , 2000, Science.

[58]  A. Arkin,et al.  Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems , 2012, Biotechnology journal.

[59]  中山 二郎,et al.  米国微生物学会コンファレンス"Cell-Cell Communication in Bacteria" に出席して , 2001 .