Dissipative biocatalytic cascades and gated transient biocatalytic cascades driven by nucleic acid networks

Abstract

Living systems consist of complex transient cellular networks guiding structural, catalytic, and switchable functions driven by auxiliary triggers, such as chemical or light energy inputs. We introduce two different transient, dissipative, biocatalytic cascades, the coupled glucose oxidase (GOx)/horseradish peroxidase (HRP) glucose–driven oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS 2− ) to the radical anion (ABTS •− ) and the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD + ) lactate–driven reduction of NAD + to NADH. The transient biocatalytic systems are driven by nucleic acid reaction modules using a nucleic acid fuel strand L 1 ′ and a nicking enzyme, Nt.BbvCI, as fuel-degrading catalyst, leading to the dynamic spatiotemporal transient formation of structurally proximate biocatalysts activating the biocatalytic cascades and transient coupled processes, including the generation of chemiluminescence and the synthesis of alanine. Subjecting the mixture of biocatalysts to selective inhibitors allows the gated transient operation of the biocatalysts. The kinetics of transient biocatalytic cascades are accompanied by kinetic models and computational simulations.

Network topology–directed design of molecular CPU for cell-like dynamic information processing

“…Dissipative strategy may also be a solution to achieve longer operation time. As reported recently by Willner and colleagues ( 61 ) and Ricci and colleagues ( 62 ), energy-dissipating reactions have been integrated with DNA strand–displacement reactions to generate some unique properties, for example, temporal reactivation of DNA systems. By integrating with these strategies, we look forward to more functional DMPS modules with longer operation time and less external fuel dependence.…”

Programming Dissipation Systems by DNA Timer for Temporally Regulating Enzyme Catalysis and Nanostructure Assembly

“…Artificial DNA structures and RNase have been integrated to formulate typical dissipation systems to redesign synthetic aptamers that can undergo chemical fuel-triggered repetitive release and loading of molecules. − Nuclease-based DNA dissipative systems have been established for sensing applications. , ATP-fueled transient DNA ligation has been utilized to regulate DNA nanostructures in a dissipative way. − In these systems, the polymerization of such transient, dynamic covalent DNA polymers with an adaptive steady state depends on ATP fuel and enzyme concentrations. Cascaded and gated DNA-based dissipation systems can be rationally designed to regulate enzyme activity. − Although some of the above examples clearly demonstrate the temporal control of the dissipation systems by species concentration and structure, an accurately temporal orchestration of the dissipative reaction network would require more robust and orthogonal molecular timers that could operate in parallel. Enzyme-involved dynamic DNA reaction networks provide easy-to-use toolboxes for temporal control. − Simmel, Winfree, and co-workers developed, in a pioneering work, a sophisticated timer/oscillator based on strand displacement reactions and enzymatic RNA production/degradation to regulate functional DNA nanodevice and RNA production .…”

Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis

“…Particularly, transient out-of-equilibrium, dissipative nucleic-acid-based networks attracted substantial recent research efforts. − Enzyme-guided transient networks driven by ligase, endonucleases, or nickases were reported, − and dynamic reaction circuits revealing oscillatory behaviors, , gated and cascaded transient operations − using dissipative reconfiguration of dynamic networks were achieved. Also, network-guided transient biocatalytic reaction modules dictating transient enzyme cascades, light-induced formation and dissipative depletion of microscale structures, e.g., microtubules, , or nanoparticle aggregates, and transient enzyme-guided release and uptake of loads were demonstrated. , …”