A Robust Electronic Switch Made of Immobilized Duplex/Quadruplex DNA

Logic-Gated Proximity Aptasensing for Cell-Surface Real-Time Monitoring of Apoptosis

In nature, intact apoptotic cells release ATP as a signaling molecule to trigger prompt phagocytic clearance, even at the earliest stage of apoptosis. Inspired by this, here we introduce a straightforward strategy for real-time monitoring ATP exocytosis and drug-stimulated apoptosis in the cancer cell surroundings. Triplex-boosted G-quadruplexes (tb-G4s) responding to cell environmental factors (H⁺ and K⁺ ) are engineered to construct a DNA logic-gated nanoplatform for proximity ATP aptasensing on the cell surface. It enables the real-time monitoring of cell apoptosis by capturing released endogenous ATP during chemotherapy drug stimulation, providing a sensitive approach for dynamically evaluating drug-induced apoptosis and therapeutic efficacy.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Inverting the G-Tetrad Polarity of a G-Quadruplex by Using Xanthine and 8-Oxoguanine

G-quadruplexes are four-stranded nucleic acid structures that are built from consecutively stacked guanine tetrad (G-tetrad) assemblies. The simultaneous incorporation of two guanine base lesions, xanthine (X) and 8-oxoguanine (O), within a single G-tetrad of a G-quadruplex was recently shown to lead to the formation of a stable G⋅G⋅X⋅O tetrad. Herein, a judicious introduction of X and O into a human telomeric G-quadruplex-forming sequence is shown to reverse the hydrogen-bond polarity of the modified G-tetrad while preserving the original folding topology. The control exerted over G-tetrad polarity by joint X⋅O modification will be valuable for the design and programming of G-quadruplex structures and their properties.

G-Quadruplex-Stimulated Optical and Electrocatalytic DNA Switches

The K(+) /18-crown-6-(or [2.2.2] cryptand)-stimulated formation and dissociation of G-quadruplex nanostructures lead to the cyclic and switchable photonic and electrocatalytic molecular devices.

Single-Molecule Visualization of the Activity of a Zn(2+)-Dependent DNAzyme

We demonstrate the single-molecule imaging of the catalytic reaction of a Zn(2+)-dependent DNAzyme in a DNA origami nanostructure. The single-molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high-speed atomic force microscopy (AFM). This nanostructure-based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single-molecule level.

DNA switches: from principles to applications

The base sequence of nucleic acid encodes structural and functional properties into the biopolymer. Structural information includes the formation of duplexes, G-quadruplexes, i-motif, and cooperatively stabilized assemblies. Functional information encoded in the base sequence involves the strand-displacement process, the recognition properties by aptamers, and the catalytic functions of DNAzymes. This Review addresses the implementation of the information encoded in nucleic acids to develop DNA switches. A DNA switch is a supramolecular nucleic acid assembly that undergoes cyclic, switchable, transitions between two distinct states in the presence of appropriate triggers and counter triggers, such as pH value, metal ions/ligands, photonic and electrical stimuli. Applications of switchable DNA systems to tailor switchable DNA hydrogels, for the controlled drug-release and for the activation of switchable enzyme cascades, are described, and future perspectives of the systems are addressed.