Powering DNA strand-displacement reactions with a continuous flow reactor

Living systems require a sustained supply of energy and nutrients to survive. These nutrients are ingested, transformed into low-energy waste products, and excreted. In contrast, synthetic DNA strand-displacement reactions typically run within closed systems provided with a finite initial supply of reactants. Once the reactants are consumed, all net reactions halt and the system ceases to function. Here we run DNA strand-displacement reactions in a continuous flow reactor, infusing fresh reactants and withdrawing waste, enabling the system to dynamically update its outputs in response to changing inputs. Running DNA strand-displacement reactions inside of continuous flow reactors allows the system to be re-used for multiple rounds of computation, which could enable the execution of more elaborate information processing tasks, including single-rail negation and sequential logic circuits.

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

[2]  Georg Seelig,et al.  DNA-Based Fixed Gain Amplifiers and Linear Classifier Circuits , 2010, DNA.

[3]  Henrike Niederholtmeyer,et al.  Implementation of cell-free biological networks at steady state , 2013, Proceedings of the National Academy of Sciences.

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

[5]  Joost Groen,et al.  Rational design of functional and tunable oscillating enzymatic networks. , 2015, Nature chemistry.

[6]  S. Rao,et al.  Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks , 2015, Journal of visualized experiments : JoVE.

[7]  Jonathan Bath,et al.  Reversible logic circuits made of DNA. , 2011, Journal of the American Chemical Society.

[8]  Vincent Noireaux,et al.  Programmable on-chip DNA compartments as artificial cells , 2014, Science.

[9]  Erik Winfree,et al.  Integrating DNA strand-displacement circuitry with DNA tile self-assembly , 2013, Nature Communications.

[10]  Evgeny Katz,et al.  Controlled Logic Gates-Switch Gate and Fredkin Gate Based on Enzyme-Biocatalyzed Reactions Realized in Flow Cells. , 2016, Chemphyschem : a European journal of chemical physics and physical chemistry.

[11]  Evgeny Katz,et al.  Reversible logic gates based on enzyme-biocatalyzed reactions and realized in flow cells: a modular approach. , 2015, Chemphyschem : a European journal of chemical physics and physical chemistry.

[12]  Erik Winfree,et al.  Catalyzed relaxation of a metastable DNA fuel. , 2006, Journal of the American Chemical Society.

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

[14]  Tom F A de Greef,et al.  Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach. , 2015, Chemical Society reviews.

[15]  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 .

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

[17]  Jing Yang,et al.  Circular DNA logic gates with strand displacement. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[18]  Dominic Scalise,et al.  Emulating cellular automata in chemical reaction–diffusion networks , 2016, Natural Computing.

[19]  Yair Glick,et al.  DNA Bipedal Motor Achieves a Large Number of Steps Due to Operation Using Microfluidics-Based Interface. , 2017, ACS nano.

[20]  Brian E. Fratto,et al.  Enzyme-Based Reversible Logic Gates Operated in Flow Cells , 2017 .

[21]  V. Manoharan,et al.  Programming colloidal phase transitions with DNA strand displacement , 2014, Science.

[22]  Jan Halámek,et al.  An enzyme-based reversible CNOT logic gate realized in a flow system. , 2014, The Analyst.

[23]  Guo-Li Shen,et al.  Fluorescence aptameric sensor for strand displacement amplification detection of cocaine. , 2010, Analytical chemistry.

[24]  G. Seelig,et al.  DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.

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

[26]  Dominic Scalise,et al.  Designing modular reaction-diffusion programs for complex pattern formation , 2014 .

[27]  Masami Hagiya,et al.  Chain Reaction Systems Based on Loop Dissociation of DNA , 2005, DNA.

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

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