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

Abstract

Fluorescent, DNA‐stabilized silver nanoclusters (DNA‐AgNCs) are applied in a range of applications within nanoscience and nanotechnology. However, their diverse optical properties, mechanism of formation, and aspects of their composition remain unexplored, making the rational design of nanocluster probes challenging. Herein, a synthetic procedure is described for obtaining a high yield of emissive DNA‐AgNCs with a C‐loop hairpin DNA sequence, with subsequent purification by size‐exclusion chromatography (SEC). Through a combination of optical spectroscopy, gel electrophoresis, inductively coupled plasma mass spectrometry (ICP‐MS), and small‐angle X‐ray scattering (SAXS) in conjunction with the systematic study of various DNA sequences, the low‐resolution structure and mechanism of the formation of AgNCs were investigated. Data indicate that fluorescent DNA‐AgNCs self‐assemble by a head‐to‐head binding of two DNA hairpins, bridged by a silver nanocluster, resulting in the modelling of a dimeric structure harboring an Ag12 cluster.

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

“…The result is consistent with the data obtained by Geczy et al about the requirement of hairpin monomer structure as an explicit requirement to generate orangeemissive AgNCs. 19 The study showed that among the size exclusion purified DNA only hairpin structures were able to generate orange emission, while dimer and other oligomeric structures failed to generate any AgNCs. 19 Furthermore, the 6C-30T-9A template was predicted to generate a 12C-bulged DNA duplex with a melting temperature of around 32 °C.…”

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

“…Because the fluorescent Ag NCs tend to self-aggregate and form large-sized silver nanoparticles, biomacromolecule DNA offers an ideal template for preparing Ag NCs with good biocompatibility . Typical ssDNA-Ag NCs are composed of several to one hundred atoms with approximately 2 nm size, which are intermediate regimes between smaller metal atoms and larger metal nanoparticles. − Compared with noble metal nanoparticles, Ag NCs exhibit unique molecular-like properties such as photoluminescence due to the discrete energy level because their size is comparable to the Fermi wavelength of electrons. − Besides, Ag NCs are becoming an appealing alternative for organic dyes and semiconductor quantum dots. So far, ssDNA-Ag NCs have been applied in numerous application fields such as biosensors, − molecular markers, ,, cell imaging, − and logic devices. , Moreover, in order to further expand the application scope of Ag NCs, the method of modulating color and fluorescence intensity is urgently needed because they have potential applications for multiplex assays.…”

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).…”

“… 42 However, the dimer of six cytosines generated by the two complete complementary strands with 6 cytosines does not form orange-emissive AgNCs, as expected. Benefiting from the important role of the third and fourth cytosines in the C-loop in base flipping, the two six-C-loop structures form head-to-head dimers via the cytosine–Ag–cytosine bridge after flipping 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.…”