Modulating the Fluorescence of Silver Nanoclusters Wrapped in DNA Hairpin Loops via Confined Strand Displacement and Transient Concatenate Ligation for Amplifiable Biosensing

Abstract

It is intriguing to modulate the fluorescence emission of DNA-scaffolded silver nanoclusters (AgNCs) via confined strand displacement and transient concatenate ligation for amplifiable biosensing of a DNA segment related to SARS-CoV-2 (s 2DNA). Herein, three stem-loop structural hairpins for signaling, recognizing, and assisting are designed to assemble a variant three-way DNA device (3WDD) with the aid of two linkers, in which orange-emitting AgNC (oAgNC) is stably clustered and populated in the closed loop of a hairpin reporter. The presence of s 2DNA initiates the toehold-mediated strand displacement that is confined in this 3WDD for repeatable recycling amplification, outputting numerous hybrid DNA-duplex conformers that are implemented for a transient “head–tail–head” tandem ligation one by one. As a result, the oAgNC-hosted hairpin loops are quickly opened in loose coil motifs, bringing a significant fluorescence decay of multiple clusters dependent on s 2DNA. Demonstrations and understanding of the tunable spectral performance of a hairpin loop-wrapped AgNC via switching 3WDD conformation would be highly beneficial to open a new avenue for applicable biosensing, bioanalysis, or clinical diagnostics.

Target DNA-Activating Proximity-Localized Catalytic Hairpin Assembly Enables Forming Split-DNA Ag Nanoclusters for Robust and Sensitive Fluorescence Biosensing

“…Short and specific DNA-templated multinuclear Ag nanoclusters (DNA/AgNCs) are formed by the stable coordination between nucleobases and reduced Ag atoms. , Because of the movement of their metal-like valence electrons among discrete electronic states, the resulting DNA/AgNC adducts exhibit intense optical absorption in biosensing and imaging. − As previously reported, the size, geometry, and electronic structure of DNA/AgNC conjugates are strongly influenced by nucleobase sequence and/or structure, thereby regulating the cluster spectra from near-ultraviolet to near-infrared. , Thus, the color and brightness of cluster adducts are drastically altered between hybridized versus single-stranded oligonucleotides. , This is the foundation to activate and “turn on” fluorescent biosensors via the affinity binding of a target DNA with a specific element, achieving greater gain in detection sensitivity. An interesting study focused on the spectra and photophysics of a green-fluorescent Ag 10 6+ cluster anchored in a two-split contiguous single-stranded oligonucleotide as the parent scaffold .…”

A Reciprocal-Amplifiable Fluorescence Sensing Platform via Replicated Hybridization Chain Reaction for Hosting Concatenated Multi-Ag Nanoclusters as Signal Reporter

“…Up to date, many attractive progresses have been witnessed in exploring the spectral behavior of mono- or multicolor DNA-AgNCs through various integration formats of recognition and signaling. Some examples are also included to investigate the fluorescence of cluster adducts synthesized in the split-parent scaffolds or at the interfacial binding sites. , Interestingly, the transient ligation of host hairpins was demonstrated in our group for the synchronous emission decay of multiple AgNC concatemers, achieving significant signal amplification . At the same time, we assembled a functional three-way DNA junction to populate multi-AgNCs in its branched arms for amplifiable ratiometric fluorescence biosensing .…”

DNA-Templated Silver Nanoclusters as Dual-Mode Sensitive Probes for Self-Powered Biosensor Fueled by Glucose

“…For example, antibacterial activity has been recently reported, which was discussed in connection with a distinct color change, a unique charge state of AgNCs@DNA leading to the production of free radicals and possibly singlet oxygen [29][30][31]. Researchers have also used phenomena such as guanine-rich DNA sequence-activated fluorescence enhancement [28,[32][33][34], aggregation-induced emission (AIE) [35], and photoinduced electron transfer (PET) [36] to design biosensing strategies using silver nanoclusters. The sensitivity of the fluorescence of AgNCs@DNA to environmental conditions prompted the development of sensors that are sensitive to heavy metals [27,[37][38][39], miRNA [28,[40][41][42], and even small molecules such as dopamine [43], melanin [44], and hydroquinone [45].…”