Formation and Structure of Fluorescent Silver Nanoclusters at Interfacial Binding Sites Facilitating Oligomerization of DNA Hairpins

Stimulus-Responsive Four-Stranded DNA Nanoring Assembly to Host Multiple Nanosilver Clusters for Cooperatively Enhanced Fluorescence Biosensing

Exploring the ability of four-stranded DNA nanorings (fsDNRs) to host multiple nanosilver clusters (NAgCs) for cooperatively amplifiable fluorescence biosensing to a specific initiator (tI*) is fascinating. By designing three DNA single strands and three analogous stem-loop hairpins, we developed a functional fsDNR through sequential cross-opening and overlapped hybridization. Note that a substrate strand (SS) was programmed with six modules: two severed splits (sT and sT') of NAgCs template, two sequestered segments by a middle unpaired spacer, and a partition for tI*-recognizable displacement, while sT and sT' were also tethered in two ends of three hairpins. At first, a triple dsDNA complex with stimulus-responsiveness was formed to guide the specific binding to tI*, while the exposed toehold of the SS activated the forward cascade hybridization of three hairpins, until the ring closure in the tailored self-assembly pathway for forming the fsDNR. The resulting four duplexes forced each pair of sT/sT' to be merged as the parent template in four nicks, guiding the preferential synthesis of four clusters in the shared fsDNR, thereby cooperatively amplifying the green fluorescence signal for sensitive assay of tI*. Meanwhile, the topological conformation of fsDNR can be stabilized by the as-formed cluster adducts to rivet the pair of two splits in the nicks. Benefitting from the self-enhanced effect of multiple emitters, this label-free fluorescent sensing strategy features simplicity, rapidity, and high on-off contrast, without involving complicated nucleic acid amplifiers.

Dual-Channel Logic Gates Operating on the Chemopalette ssDNA-Ag NCs/GO Nanocomposites

In this work, we demonstrate that the emission wavelength and intensity of silver nanoclusters (Ag NCs) can be facilely tuned by the configuration transformation from the adsorption of Ag NCs to the graphene oxide (GO) surface to the desorption of Ag NCs from GO. Bicolor Ag NCs tethering the complementary sequence of influenza A virus genes are prepared, named green-emitting G-Ag NCs-CH5N1 (530 nm) and red-emitting R-Ag NCs-CH1N1 (589 nm). As for the high affinity of the complementary fragment of genes to GO, the adsorption of Ag NCs to GO leads to the formation of G-Ag NCs-CH5N1/GO and R-Ag NCs-CH1N1/GO nanocomposites, leading to fluorescent quenching due to energy transfer. By conjugating complementary sequences as capturing probes for targets, the formation of genes/Ag NC duplex-stranded structures results in the desorption of Ag NCs from GO, activating the fluorescence signal. More interestingly, compared with sole single-stranded DNA-templated fluorescent Ag NCs (ssDNA-Ag NCs), the activatable emission wavelength of the G-Ag NCs-CH5N1/H5N1 complex exhibits a notable red shift (555 nm) with a 49% recovery rate, while that of the R-Ag NCs-CH1N1/H1N1 complex shows a distinct blue shift (569 nm) with a 200% recovery rate. Via target-responsive configuration transformation of Ag NCs/GO hybrid materials, the emission wavelength and intensity of Ag NCs are effectively regulated. Based on the output changes according to different input combinations, novel dual-channel logic gates for multiplex simultaneous detection are developed by using the tunable color and intensity of ssDNA-Ag NCs. Our observation may open a new path for multiplex analysis in a facile and rapid way combining the logic gate strategy.

The spatial organization of trace silver atoms on a DNA template

DNA with programmable information can be used to encode the spatial organization of silver atoms. Based on the primary structures of a DNA template containing a controllable base arrangement and number, the surrounding environment and cluster together can induce the folding of the DNA template into an appropriate secondary structure for forming AgNCs with different fluorescence emissions, such as i-motif, G-quadruplex, dimeric template, triplex, monomeric or dimeric C-loop, emitter pair, and G-enhancer/template conjugate. Stimuli can induce the dynamic structural transformation of the DNA template with a recognition site for favourably or unfavourably forming AgNCs, along with varied fluorescence intensities and colours. The array of several or more of the same and different clusters can be performed on simple and complex nanostructures, while maintaining their original properties. By sorting out this review, we systematically conclude the link between the performance of AgNCs and the secondary structure of the DNA template, and summarize the precise arrangement of nanoclusters on DNA nanotechnology. This clear review on the origin and controllability of AgNCs based on the secondary structure of the DNA template is beneficial for exploring the new probe and optical devices.

Efficient Editing of Silver Nanoclusters by Changing Simply One Cytosine in a DNA Template

DNA with genetic information was edited to regulate and repair the structure and function of a protein. In DNA nanotechnology, DNA with programmable information can be designed to edit the fluorescence intensity and emissive colors of DNA-stabilized silver nanoclusters (DNA/AgNCs). By introducing and moving one cytosine in the spacer of the emitter domain, we have built up a simple strategy to regulate the excitation and emission wavelengths of AgNCs. When replacing thymine in the spacer of the emitter with one cytosine, the expected excitation and emission change do not occur. However, after moving the introduced cytosine, DNA templates produce AgNCs with extremely different excitation and emission wavelengths from those of the initial template, leading to a template for near-infrared (NIR) emissive species with the highest fluorescence intensity. The formation of AgNCs induces the DNA template into condensed secondary structure based on an altered migration rate in PAGE. The simple strategy of moving one cytosine in a spacer in the emitter domain can enrich the library of templates for synthesizing diverse DNA/AgNCs and has great potential in bioimaging and probe design.