The structural shift of a DNA template between a hairpin and a dimer tunes the emission color of DNA-templated AgNCs

Shah, Pratik; Choi, Sukwon; Nagda, Riddhi; Geczy, Reka; Cho, Seok Keun; Bhang, Yong Joo; Kim, Tae-Hwan; Song, Tae Yong; Lee, Phil Hyu; Kang, Ju Hee; Thulstrup, Peter W.; Bjerrum, Morten J.; Jung, Il Lae; Yang, Seong Wook

doi:10.1039/c8nr06186f

Cited by 27 publications

(28 citation statements)

References 34 publications

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“…Therefore, depending on the GC content of the sequence, anchor lengths can be modulated which allows this sensor design to be universal for the detection of various miRNA sequences as demonstrated previously [13]. Moreover, we showed that the emission wavelength of the encapsulated AgNCs could be modulated by altering the secondary structure of DNA/AgNCs [24]. Thus, we investigated whether the secondary structure of DNA/AgNCs influences the photo-stability of emissive AgNCs.…”

Section: Resultsmentioning

confidence: 89%

“…Based on our previous study [13,24], we further analyzed the secondary structures of DNA/AgNCs templates using in-gel fluorescence assay, to see whether the secondary structures are correlated to the color of fluorescence. Indeed, we found that the secondary structure of DNA 6C-217-11bp is a dimer, while DNA 6C-27a-3bp generated a hairpin structure (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, we recently reported that if the secondary structure of a DNA template is given, either a dimer or hairpin, it uniformly determines the emission colors, of the DNA template. When a DNA/AgNCs template forms dimer structure, it prefers to encapsulate orange emissive AgNCs, while when a template forms a hairpin structure, it prefers to encapsulate red emissive AgNCs [24]. Further multiple previous studies have indicated that the red emissive AgNCs are more prone to oxidation by O 2 [21,25].…”

Section: Introductionmentioning

confidence: 99%

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Structural Influence on the Post-Clustering Stability of DNA/AgNCs Fluorescence

et al. 2019

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DNA-encapsulated Silver Nanoclusters (DNA/AgNCs) based sensors have gained increasing attention in past years due to their diverse applications in bioimaging, biosensing, and enzymatic assays. Given the potential of DNA/AgNCs for practical applications, the systematic studies of the fluorescent stability over an extended period is necessary. However, the correlation between nucleic acid properties and the long-term stability of DNA/AgNCs is less known. With locking-to-unlocking sensors, in which the secondary structure of DNA template is standardized, we investigated the correlation between the DNA structure and the fluorescence stability of AgNCs. Post-synthesis of DNA/AgNCs, the fluorescence, and structures of templates were monitored over three weeks. By combining the fluorescence spectroscopy with the in-gel fluorescent assay, we found that AgNCs encapsulated by dimer-structured DNA/AgNCs templates were more stable than those of hairpin-structured DNA/AgNCs templates. While the orange fluorescence from the dimer templates increased over three weeks, the red fluorescence from the hairpin templates was diminished by >80% within two days at room temperature. Further tests revealed that hairpin-encapsulated red-emissive AgNCs is more sensitive to oxidation by atmospheric oxygen compared to dimer encapsulated orange AgNCs. Our observations may provide an important clue in encapsulating photophysically more stable AgNCs by tuning the DNA secondary structures. The proposed strategy here can be essential for pragmatic applications of DNA/AgNCs templates.

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structural Influence on the Post-Clustering Stability of DNA/AgNCs Fluorescence

et al. 2019

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“…As an important factor affecting the emission of DNA-AgNCs, the modulation of secondary DNA structures was used in the ratio detection system (Shah et al, 2018). Xu et al developed a proportional visual analysis sensor platform for miRNA-21 in cells based on the self-assembly of AgNCs triggered by chain displacement.…”

Section: The Fluorescence Signal Based On Dna Strand Hybridizationmentioning

confidence: 99%

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

Yang

et al. 2020

Front. Chem.

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Recently years have witnessed a surge in application of DNA-AgNCs in optics, catalysis, sensing, and biomedicine. DNA-templated silver nanoclusters (DNA-AgNCs), as emerging fluorophores, display superior optical performance since their size is close to the Fermi wavelength. DNA-AgNCs possess unique features, including high fluorescence quantum yields and stability, biocompatibility, facile synthesis, and low toxicity, which are requisite for fluorescent probes. The fluorescent emission of DNA-AgNCs can cover the violet to near-infrared (NIR) region by varying the DNA sequences, lengths, and structures or by modifying the environmental factors (such as buffer, pH, metal ions, macromolecular polymers, and small molecules). In view of the above excellent properties, we overview the DNA-AgNCs from the viewpoints of synthesis and fluorescence properties, and summarized its biological applications of fluorescence sensing and imaging.

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“…[26] Fort his class of AgNCbased sensor, it has been reported that they can be emissive both in am onomeric and dimeric state,d epending on the sequence. [27] We here investigate the impact of AgNC formation on oligonucleotide tertiary structure.S pecifically, we hypothesize that dimerization and oligomerization of short monomeric hairpin DNAs occur upon the reduction of coordinated Ag I .W er eport the first small-angle X-ray scattering (SAXS) study of DNA-AgNCs structure in solution, as well as the production of circular oligonucleotide hairpins that support amodel with an interfacial binding motif for AgNCs.W ep ropose that AgNCs bridge two hairpin oligonucleotides,w here the self-assembly of the dimeric complex converts dark AgNCs into the highly fluorescent AgNC species.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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The structural shift of a DNA template between a hairpin and a dimer tunes the emission color of DNA-templated AgNCs

Abstract: The structural shift of a DNA hairpin-dimer is as important as the DNA sequence in determining the fluorescent properties of DNA-stabilized silver nanoclusters (DNA/AgNCs).

Cited by 27 publications

References 34 publications

Structural Influence on the Post-Clustering Stability of DNA/AgNCs Fluorescence

Structural Influence on the Post-Clustering Stability of DNA/AgNCs Fluorescence

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

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

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