Controllable DNA strand displacement by independent metal-ligand complexation

DNAzyme-Based Dissipative DNA Strand Displacement for Constructing Temporal Logic Gates

Toehold-mediated DNA strand displacement is the foundation of dynamic DNA nanotechnology, encompassing a wide range of tools with diverse functions, dynamics, and thermodynamic properties. However, a majority of these tools are limited to unidirectional reactions driven by thermodynamics. In response to the growing field of dissipative DNA nanotechnology, we present an approach: DNAzyme-based dissipative DNA strand displacement (D-DSD), which combines the principles of dynamic DNA nanotechnology and dissipative DNA nanotechnology. D-DSD introduces circular and dissipative characteristics, distinguishing it from the unidirectional reactions observed in conventional strand displacement. We investigated the reaction mechanism of D-DSD and devised temporal control elements. By substituting temporal components, we designed two distinct temporal AND gates using fewer than 10 strands, eliminating the need for complex network designs. In contrast to previous temporal logic gates, our temporal storage is not through dynamics control or cross-inhibition but through autoregressive storage, a more modular and scalable approach to memory storage. D-DSD preserves the fundamental structure of toehold-mediated strand displacement, while offering enhanced simplicity and versatility.

Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases

Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH-A base pair and a metal-mediated UOH-GdIII-UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH-A and UOH-GdIII-UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.

Programming Non-Nucleic Acid Molecules into Computational Nucleic Acid Systems

Nucleic acid (NA) computation has been widely developed in the past years to solve kinds of logic and mathematic issues in both information technologies and biomedical analysis. However, the difficulty to integrate non-NA molecules limits its power as a universal platform for molecular computation. Here, we report a versatile prototype of hybridized computation integrated with both nucleic acids and non-NA molecules. Employing the conformationally controlled ligand converters, we demonstrate that non-NA molecules, including both small molecules and proteins, can be computed as nucleic acid strands to construct the circuitry with increased complexity and scalability, and can be even programmed to solve arithmetical calculations within the computational nucleic acid system. This study opens a new door for molecular computation in which all-NA circuits can be expanded with integration of various ligands, and meanwhile, ligands can be precisely programmed by the nuclei acid computation.

Cofactor-assisted three-way DNA junction-driven strand displacement

Toehold-mediated strand displacement is widely used to construct and operate DNA nanodevices. Cooperative regulation of strand displacement with diverse factors is pivotal in the design and construction of functional and dynamic devices. Herein, a cofactor-assisted three-way DNA junction-driven strand displacement strategy was reported, which could tune the reaction kinetics by the collaboration of DNA and other types of stimulus. This strategy is responsive to various inputs by incorporation of the specific sequence into the three-way junction structure. Specifically, the cooperation of multiple factors changes the conformation of the specific domain and promotes the reaction. To demonstrate the strategy, adenosine triphosphate (ATP), HG²⁺, and pH were used as cofactors to modulate the displacement reaction. The electrophoresis and fluorescence experiments showed that the cooperative regulation of the strand displacement reaction could be achieved by diverse factors using this strategy. The proposed strategy provides design flexibility for dynamic DNA devices and may have potential in biosensing and biocomputing.

Cooperative regulation of strand displacement with diverse factors was achieved by a cofactor-assisted three-way DNA junction-driven strategy. Using this strategy nanodevices reacted to various inputs by incorporating a specific sequence into the three-way junction structure.