Literature DB >> 29242317

Enzyme-free nucleic acid dynamical systems.

Niranjan Srinivas1, James Parkin2, Georg Seelig3, Erik Winfree4,2,5, David Soloveichik6.   

Abstract

Chemistries exhibiting complex dynamics-from inorganic oscillators to gene regulatory networks-have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages.
Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2017        PMID: 29242317     DOI: 10.1126/science.aal2052

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  41 in total

Review 1.  Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity.

Authors:  Tulsi Ram Damase; Peter B Allen
Journal:  Bioconjug Chem       Date:  2019-01-03       Impact factor: 4.774

2.  Effective design principles for leakless strand displacement systems.

Authors:  Boya Wang; Chris Thachuk; Andrew D Ellington; Erik Winfree; David Soloveichik
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-13       Impact factor: 11.205

3.  Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts.

Authors:  Tarryn E Miller; Thomas Beneyton; Thomas Schwander; Christoph Diehl; Mathias Girault; Richard McLean; Tanguy Chotel; Peter Claus; Niña Socorro Cortina; Jean-Christophe Baret; Tobias J Erb
Journal:  Science       Date:  2020-05-08       Impact factor: 47.728

4.  Nucleic Acid Strand Displacement with Synthetic mRNA Inputs in Living Mammalian Cells.

Authors:  Gourab Chatterjee; Yuan-Jyue Chen; Georg Seelig
Journal:  ACS Synth Biol       Date:  2018-11-20       Impact factor: 5.110

5.  A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.

Authors:  Stefan Badelt; Casey Grun; Karthik V Sarma; Brian Wolfe; Seung Woo Shin; Erik Winfree
Journal:  J R Soc Interface       Date:  2020-06-03       Impact factor: 4.118

6.  Noise control for molecular computing.

Authors:  Tomislav Plesa; Konstantinos C Zygalakis; David F Anderson; Radek Erban
Journal:  J R Soc Interface       Date:  2018-07       Impact factor: 4.118

Review 7.  Programmable protein circuit design.

Authors:  Zibo Chen; Michael B Elowitz
Journal:  Cell       Date:  2021-04-12       Impact factor: 41.582

8.  Fuel-Driven Transient DNA Strand Displacement Circuitry with Self-Resetting Function.

Authors:  Jie Deng; Andreas Walther
Journal:  J Am Chem Soc       Date:  2020-12-02       Impact factor: 15.419

9.  Dynamic self-assembly of compartmentalized DNA nanotubes.

Authors:  Siddharth Agarwal; Melissa A Klocke; Passa E Pungchai; Elisa Franco
Journal:  Nat Commun       Date:  2021-06-11       Impact factor: 14.919

10.  Controllable DNA strand displacement by independent metal-ligand complexation.

Authors:  Liang-Liang Wang; Qiu-Long Zhang; Yang Wang; Yan Liu; Jiao Lin; Fan Xie; Liang Xu
Journal:  Chem Sci       Date:  2021-05-18       Impact factor: 9.825

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