Literature DB >> 28135261

Microscopic agents programmed by DNA circuits.

G Gines1,2, A S Zadorin2,3, J-C Galas3, T Fujii1, A Estevez-Torres3, Y Rondelez1,2.   

Abstract

Information stored in synthetic nucleic acids sequences can be used in vitro to create complex reaction networks with precisely programmed chemical dynamics. Here, we scale up this approach to program networks of microscopic particles (agents) dispersed in an enzymatic solution. Agents may possess multiple stable states, thus maintaining a memory and communicate by emitting various orthogonal chemical signals, while also sensing the behaviour of neighbouring agents. Using this approach, we can produce collective behaviours involving thousands of agents, for example retrieving information over long distances or creating spatial patterns. Our systems recapitulate some fundamental mechanisms of distributed decision making and morphogenesis among living organisms and could find applications in cases where many individual clues need to be combined to reach a decision, for example in molecular diagnostics.

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Year:  2017        PMID: 28135261     DOI: 10.1038/nnano.2016.299

Source DB:  PubMed          Journal:  Nat Nanotechnol        ISSN: 1748-3387            Impact factor:   39.213


  49 in total

Review 1.  Quorum sensing: cell-to-cell communication in bacteria.

Authors:  Christopher M Waters; Bonnie L Bassler
Journal:  Annu Rev Cell Dev Biol       Date:  2005       Impact factor: 13.827

2.  Scaling down DNA circuits with competitive neural networks.

Authors:  Anthony J Genot; Teruo Fujii; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2013-06-12       Impact factor: 4.118

3.  Spatial waves in synthetic biochemical networks.

Authors:  Adrien Padirac; Teruo Fujii; André Estévez-Torres; Yannick Rondelez
Journal:  J Am Chem Soc       Date:  2013-06-20       Impact factor: 15.419

4.  High-throughput and long-term observation of compartmentalized biochemical oscillators.

Authors:  Koshi Hasatani; Mathieu Leocmach; Anthony J Genot; André Estévez-Torres; Teruo Fujii; Yannick Rondelez
Journal:  Chem Commun (Camb)       Date:  2013-08-05       Impact factor: 6.222

5.  Synthesis of programmable reaction-diffusion fronts using DNA catalyzers.

Authors:  Anton S Zadorin; Yannick Rondelez; Jean-Christophe Galas; André Estevez-Torres
Journal:  Phys Rev Lett       Date:  2015-02-09       Impact factor: 9.161

6.  Bottom-up construction of in vitro switchable memories.

Authors:  Adrien Padirac; Teruo Fujii; Yannick Rondelez
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-29       Impact factor: 11.205

7.  Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

Authors:  Valeriya N Antipova; Lyudmila A Zheleznaya; Nadezhda V Zyrina
Journal:  FEMS Microbiol Lett       Date:  2014-07-14       Impact factor: 2.742

8.  Simultaneous elimination of carryover contamination and detection of DNA with uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification (UDG-LAMP).

Authors:  Kuangwen Hsieh; Peter L Mage; Andrew T Csordas; Michael Eisenstein; H Tom Soh
Journal:  Chem Commun (Camb)       Date:  2014-02-28       Impact factor: 6.222

9.  Programming an in vitro DNA oscillator using a molecular networking strategy.

Authors:  Kevin Montagne; Raphael Plasson; Yasuyuki Sakai; Teruo Fujii; Yannick Rondelez
Journal:  Mol Syst Biol       Date:  2011-02-01       Impact factor: 11.429

10.  Synthetic in vitro transcriptional oscillators.

Authors:  Jongmin Kim; Erik Winfree
Journal:  Mol Syst Biol       Date:  2011-02-01       Impact factor: 11.429

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  25 in total

1.  Consecutive feedback-driven constitutional dynamic networks.

Authors:  Liang Yue; Shan Wang; Verena Wulf; Sivan Lilienthal; Françoise Remacle; R D Levine; Itamar Willner
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-06       Impact factor: 11.205

2.  Synthesis and materialization of a reaction-diffusion French flag pattern.

Authors:  Anton S Zadorin; Yannick Rondelez; Guillaume Gines; Vadim Dilhas; Georg Urtel; Adrian Zambrano; Jean-Christophe Galas; André Estevez-Torres
Journal:  Nat Chem       Date:  2017-05-01       Impact factor: 24.427

3.  Switches induced by quorum sensing in a model of enzyme-loaded microparticles.

Authors:  Tamás Bánsági; Annette F Taylor
Journal:  J R Soc Interface       Date:  2017-03       Impact factor: 4.118

4.  Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks.

Authors:  Samuel W Schaffter; Kuan-Lin Chen; Jackson O'Brien; Madeline Noble; Arvind Murugan; Rebecca Schulman
Journal:  Nat Chem       Date:  2022-08-04       Impact factor: 24.274

Review 5.  Dissipative DNA nanotechnology.

Authors:  Erica Del Grosso; Elisa Franco; Leonard J Prins; Francesco Ricci
Journal:  Nat Chem       Date:  2022-06-06       Impact factor: 24.274

6.  Programmable synthetic cell networks regulated by tuneable reaction rates.

Authors:  Adrian Zambrano; Giorgio Fracasso; Mengfei Gao; Martina Ugrinic; Dishi Wang; Dietmar Appelhans; Andrew deMello; T-Y Dora Tang
Journal:  Nat Commun       Date:  2022-07-06       Impact factor: 17.694

Review 7.  Viewpoint: From Responsive to Adaptive and Interactive Materials and Materials Systems: A Roadmap.

Authors:  Andreas Walther
Journal:  Adv Mater       Date:  2019-11-25       Impact factor: 30.849

8.  Photochemical Control over Oscillations in Chemical Reaction Networks.

Authors:  Aleksandr A Pogodaev; Albert S Y Wong; Wilhelm T S Huck
Journal:  J Am Chem Soc       Date:  2017-10-19       Impact factor: 15.419

9.  A chemical circular communication network at the nanoscale.

Authors:  Beatriz de Luis; Ángela Morellá-Aucejo; Antoni Llopis-Lorente; Tania M Godoy-Reyes; Reynaldo Villalonga; Elena Aznar; Félix Sancenón; Ramón Martínez-Máñez
Journal:  Chem Sci       Date:  2020-12-09       Impact factor: 9.825

10.  Probabilistic switching circuits in DNA.

Authors:  Daniel Wilhelm; Jehoshua Bruck; Lulu Qian
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-16       Impact factor: 11.205

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