Silver Nanoclusters Serve as Fluorescent Rivets Linking Hoogsteen Triplex DNA and Hairpin-Loop DNA Structures

Abstract

Greater understanding of the mutual influence between DNA and the associated nanomaterial on the properties of each other can provide alternative strategies for designing and developing DNA nanomachines. DNA secondary structures are essential for encapsulating highly emissive silver nanoclusters (DNA/AgNCs). Likewise, AgNCs stabilize secondary DNA structures, such as hairpin DNA, duplex DNA, and parallel-motif DNA triplex. In this study, we found that the fluorescence of AgNCs encapsulated within a Hoogsteen triplex DNA structure can be turned on and off in response to pH changes. We also show that AgNCs can act as nanoscale rivets, linking two functionally distinctive DNA nanostructures. For instance, we found that a Hoogsteen triplex DNA structure with a seven-cytosine loop encapsulates red fluorescent AgNCs. The red fluorescence faded under alkaline conditions, whereas the fluorescence was restored in a near-neutral environment. Hairpin DNA and random DNA structures did not exhibit this pH-dependent AgNCs fluorescence. A fluorescence lifetime measurement and a small-angle X-ray scattering analysis showed that the triplex DNA-encapsulated AgNCs were photophysically convertible between bright and dark states. An in-gel electrophoresis analysis indicated that bright and dark convertibility depended on the AgNCs-riveted dimerization of the triplex DNAs. Moreover, we found that AgNCs rivet the triplex DNA and hairpin DNA to form a heterodimer, emitting orange fluorescence. Our findings suggest that AgNCs between two cytosine-rich loops can be used as nanorivets in designing noncanonical DNA origami beyond Watson–Crick base pairing.

Dual-Modal Lateral Flow Test Strip Assisted by Near-Infrared-Powered Nanomotors for Direct Quantitative Detection of Circulating MicroRNA Biomarkers from Serum

“…Moreover, the single-base mutated miRNA-21 also produced a slight increase in the thermal signal (29.1 °C), which was nearly negligible compared to the intense signal induced by miRNA-21. The likely explanation for the result was that the heating effect (<57.8 °C) in rection buffer under NIR irradiation significantly reduced the probability of nonspecific hybridization even for single base-pair without affecting the structure of hDNA. , These results strongly validated the selectivity of the designed LFTS in specific detection of miRNA-21 targets.…”

“…The likely explanation for the result was that the heating effect (<57.8 °C) in rection buffer under NIR irradiation significantly reduced the probability of nonspecific hybridization even for single base-pair without affecting the structure of hDNA. 39,40 These results strongly validated the selectivity of the designed LFTS in specific detection of miRNA-21 targets.…”

Fluorescent Features and Applicable Biosensing of a Core–Shell Ag Nanocluster Shielded by a DNA Tetrahedral Nanocage

“…Typically, specific C-rich DNA-templated silver nanoclusters (DNA/AgNCs) are prepared through the redox reaction of Ag + ions that preferably coordinate with these polymeric ligands via their nucleobases. The locally concentrated Ag + adducts are chemically reduced, allowing the agglomeration of Ag 0 to form DNA/AgNCs. − The DNA/AgNCs entity develops discrete and sparsely organized electronic states and becomes an optical chromophore. Because of the strong molecular brightness, robust emission, high quantum yields (QYs), and long fluorescence lifetimes, these label-free emitters have been an intriguing class of fluorescent probes with well-defined perspectives for applications in the biological sensing of disease-related markers at ultralow levels, , enzyme activity, cellular imaging, and environment or food analysis .…”

Ratiometric Fluorescence Biosensing of Tandem Biemissive Ag Clusters Boosted by Confined Catalytic DNA Assembly

“…As a promising label-free fluorophore, DNA-templated Ag clusters (DNA/AgCs) have been confirmed with inherent advantages such as strong optical absorption, high quantum yield, tunable spectral emission, good biocompatibility, and low cost. − A variety of cytosine (C)-rich template sequences have been engineered for populating DNA/AgCs, on which Ag + ions preferably coordinate with C bases and then are reduced to form emissive cluster/nucleobase adducts. The change of the DNA template component and length determines the clusters’ number and geometry and therefore electronic structure and adjusts their color and brightness. , The clustering scaffolds and recognizable elements can be readily designed and programmed in diverse DNA-based probes, structures, or devices. − Once presenting a specific target, the molecular binding event is activated to guide their conformation switches; thus, the template sequences are liberated or locked at precise positions to develop or dissociate these fluorescent adducts, further modulating their emission spectra for tailored signaling modes. For example, Miao’s group reported chameleon Ag clusters through the directional disassembly of hairpin structures to construct logic operations or ratiometric sensing platforms. , Owing to the intrinsic built-in correction capable of minimizing false positive backgrounds, dual-color DNA/AgCs as ratiometric signal reporters are more desirable for accurately sensing a univariate target than a single cluster emitter. − By encoding the host templates in a shared DNA tweezer or three-way junction, we have explored the ratiometric fluorescence of bicolor Ag clusters under a target-stimulated conformation switch. − The ability of two clusters with configuration responsiveness from molecule-recognizing events enables accurate fluorescent assay of analytes at the ultralow level.…”