Noncanonical Head-to-Head Hairpin DNA Dimerization Is Essential for the Synthesis of Orange Emissive Silver Nanoclusters

Abstract

DNA secondary structures, such as dimers and hairpins, are important for the synthesis of DNA templateembedded silver nanoclusters (DNA/AgNCs). However, the arrangement of AgNCs within a given DNA template and how the AgNC influences the secondary structure of the DNA template are still unclear. Here, we introduce a noncanonical head-to-head hairpin DNA nanostructure that is driven by orange-emissive AgNCs. Through detailed in-gel analysis, sugar backbone switching, inductively coupled plasma mass spectrometry, small-angle X-ray scattering, and small angle neutron scattering, we show that the orange-emissive AgNCs mediate cytosine-Ag-cytosine bridging between two six-cytosine loop (6C-loop) hairpin DNA templates. Unlike green, red, or far-red emissive AgNCs, which are embedded inside a hairpin and duplex DNA template, the orange-emissive AgNCs are localized on the interface between the two 6C-loop hairpin DNA templates, thereby linking them. Moreover, we found that deoxyribose in the backbone of the 6C-loop at the third and fourth cytosines is crucial for the formation of the orange-emissive AgNCs and the head-to-head hairpin DNA structure. Taken together, we suggest that the specific wavelength of AgNCs fluorescence is determined by the mutual interaction between the secondary or tertiary structures of DNA-and AgNC-mediated intermolecular DNA cross-linking.

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

“…[44] Ac oncurrent study on the same type of 6C hairpin systems has confirmed the presented findings and provides further insight into the detailed requirements for formation of self-assembly of emissive hairpin dimers. [45] Angewandte Chemie Forschungsartikel Figure 5. SAXS data (*)a nd predictions( blue lines) from the molecular models of the 6C-miR-21-10bp AgNC-DNA dimer (right) and unmodified monomer (left).…”

The spatial organization of trace silver atoms on a DNA template

“…Beneting from the important role of the third and fourth cytosines in the C-loop in base ipping, the two six-C-loop structures form head-to-head dimers via the cytosine-Ag-cytosine bridge aer ipping base to implement the formation of orange emissive AgNCs 43,44 (no. 7 in Table 2).…”

“…In recent years, some approaches revealed that the formation of AgNCs depend largely on the specic secondary structure by interaction of the protonation, base-pairing, and cluster-DNA, further highlighting the role of the secondary structure in regulating the properties of AgNCs. [40][41][42][43][44] Consequently, it is necessary to integrate recent progresses with the acknowledged mechanism and summarize again the direct link between the silver atom organization on the DNA secondary structure and the performance of AgNCs, and the stimuli-responsive dynamic performance of AgNCs based on the change of the DNA secondary structure, providing an all-round support for understanding the origin of DNA/AgNCs.…”

The Fluorescent Palette of DNA-Templated Silver Nanoclusters for Biological Applications

“…In addition, the relationship between the structural and fluorescence emission of DNA-AgNCs was also studied. Recently, Shah et al (2020) reported that the orange emitting AgNCs were localized on the interface via a headto-head binding of two DNA hairpins, while green, red, or NIR emissive AgNCs were embedded in a hairpin and double stranded DNA templates. The hairpin DNA can convert into G-quadruplex (G 4 ) or i-motif structures, while the G 4 -AgNCs only showed intense peaks and the i-motif AgNCs exhibited poor peaks (Li et al, 2011).…”