Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks

Abstract

The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.

Recent Advances in DNA Nanostructures Applied in Sensing Interfaces and Cellular Imaging

“…Besides the traditional Watson–Crick base pairing-based nucleic acids, various features of the base constituents provide diverse alternative principles to influence the structure and function of nucleic acids. − These principle mechanisms include switchable reconfiguration G-rich strands into the G-quadruplex unit, with the assistance of K + and their separation by crown-ether; ,, stabilization/destabilization of photoisomerizer-intercalated DNA duplex, for example the trans- / cis- azobenzene molecule units; − and the hydrogen bond-stabilized DNA triplex structures . In all these structures, the G-quadruplex attracts significant attention as the functional nanounit in chemistry, biology, and nanotechnology, especially in the biosensing research field. − As shown in Figure A, Li and co-workers monitored the electrochemical behavior of a single G-quadruplex nanostructure intercalated with hemin, G-quadruplex/hemin DNAzyme, to mimick HRP catalytic function on a gold surface . In the presence of targeted miRNA, the G-quadruplex nanostructure was formed on the gold surface, oxidizing hydroquinone (HQ) present in the sample solution to benzoquinone (BQ) by H 2 O 2 that is catalyzed by G-quadruplex/hemin DNAzyme.…”

Switchable and dynamic G-quadruplexes and their applications

“…89 Such systems require the design of reaction cycles that involve the triggered formation of out-of-equilibrium intermediate modules accompanied by the eventual degradation of these intermediate species to waste products, thus leading to recovery of the initial state of the system over time. Such reaction modules leading to the transient formation of Gquadruplexes were designed, 88 L 1 /T 1 duplex. The released strand, E 1 , disassembles the intermediate hemin/G-quadruplex by hybridization with G 1 to form the parent reaction module consisting of L 1 /T 1 and G 1 /E 1 .…”

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 .…”