DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Rolband, Lewis; Yourston, Liam; Chandler, Morgan; Beasock, Damian; Danai, Leyla; Kozlov, Seraphim; Marshall, Nolan; Shevchenko, O.A.; Krasnoslobodtsev, Alexey V.; Afonin, Kirill A.

doi:10.3390/molecules26134045

Cited by 20 publications

(60 citation statements)

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“…Our previously published data suggested that the formation of alternative DNA structures via strong silver mediated C-Ag-C base paring results in heterogeneity of DNA-AgNC populations [6]. HL nucleic acid structures appear to improve the results by forming a homogeneous, both structurally and optically, population of AgNCs [23]. HL consists of a base-paired stem and a loop sequence with unpaired nucleotide bases (Figure 1A) and represent a key building block of many folded RNA secondary structures found in nature, including ribozymes and messenger-RNA [24].…”

Section: Design Of the Hairpin-loop Agnc Dna Templatementioning

confidence: 96%

“…AgNCs are highly susceptible to oxidation with dramatic changes in optical properties of the nanoclusters [6]. A closed geometry of DNA/RNA templates results in an improved stability of AgNCs against oxidative species present in solution, including dissolved oxygen [7,23]. Looped templates used in the current study, therefore, provide additional advantages of increased AgNCs stability.…”

Section: Design Of the Hairpin-loop Agnc Dna Templatementioning

confidence: 97%

“…Our choice of loop sizes spanned from C 7 to C 19 with a +2C increment. Although other designs have been utilized for sensing Hg 2+ [26], we have chosen to work with DNA HL templates to avoid structural and functional uncertainties [23] and to make the structures suitable for further implementation into larger nano-designs [6,7]. AgNCs are highly susceptible to oxidation with dramatic changes in optical properties of the nanoclusters [6].…”

Section: Design Of the Hairpin-loop Agnc Dna Templatementioning

confidence: 99%

“…Recent reports also indicate that DNA-AgNC emissions are not limited to just a visible spectral range, but also extend into UV as well as NIR portions of the electromagnetic spectrum [4,6,27,28]. Various sizes of C N loops generate DNA-AgNCs with distinct fluorescence patterns [22,23]. Figure 2 shows the excitation-emission plots (EEMs) for AgNCs templated on hairpins with C 7 , C 9 , C 11 , C 13 , C 15 , C 17 , and C 19 loop sizes.…”

Section: Optical Properties Of Agncs Templated By Various Hairpin-loop Dna Templatesmentioning

confidence: 99%

“…Herein, we tested various sizes of cytosine-rich hairpin-loop structures for their ability to template stable and well-defined fluorescence patterns. Hairpin-loop DNA templates provide reproducibility in making AgNCs by removing structural ambiguity inherent to ss-C N templating sequences [6,22,23]. Such properties as AgNC's stability and reproducibility of fluorescence signals are desirable for the use of DNA-AgNC as biosensors.…”

Section: Introductionmentioning

confidence: 99%

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Hg2+ Detection with Rational Design of DNA-Templated Fluorescent Silver Nanoclusters

et al. 2021

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Atomically precise silver nanoclusters (AgNCs) are small nanostructures consisting of only a few atoms of silver. The combination of AgNCs with cytosine-rich single-stranded oligonucleotides results in DNA-templated silver nanoclusters (DNA-AgNCs). DNA-AgNCs are highly luminescent and can be engineered with reproducible and unique fluorescent properties. Furthermore, using nucleic acids as templates for the synthesis of AgNCs provides additional practical benefits by expanding optical activity beyond the visible spectral range and creating the possibility for color tunability. In this study, we explore DNA oligonucleotides designed to fold into hairpin-loop (HL) structures which modulate optical properties of AgNCs based on the size of the loop containing different number of cytosines (HL-CN). Depending on the size of the loop, AgNCs can be manufactured to have either single or multiple emissive states. Such hairpin-loop structures provide an additional stability for AgNCs and further control over the base composition of the loop, allowing for the rational design of AgNCs’ optical properties. We demonstrate the potential of AgNCs in detecting Hg2+ by utilizing the HL-C13 design and its variants HL-T2C11, HL-T4C9, and HL-T6C7. The replacement of cytosines with thymines in the loop was intended to serve as an additional sink for mercury ions extending the detectable range of Hg2+. While AgNC@HL-T0C13 exhibits an interpretable quenching curve, AgNC@HL-T6C7 provides the largest detectable range of Hg2+. The results presented herein suggest that it is possible to use a rational design of DNA-AgNCs based on the composition of loop sequence in HL structures for creating biosensors to detect heavy metals, particularly Hg2+.

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Section: Design Of the Hairpin-loop Agnc Dna Templatementioning

confidence: 96%

Section: Design Of the Hairpin-loop Agnc Dna Templatementioning

confidence: 97%

Section: Design Of the Hairpin-loop Agnc Dna Templatementioning

confidence: 99%

Section: Optical Properties Of Agncs Templated By Various Hairpin-loop Dna Templatesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Hg2+ Detection with Rational Design of DNA-Templated Fluorescent Silver Nanoclusters

et al. 2021

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Detection of cancer‐associated miRNA using a fluorescence switch of AgNC@NA and guanine‐rich overhang sequences

2023

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DNA-templated silver nanoclusters (AgNC@DNA) are a novel type of nanomaterial with advantageous optical properties. Only a few atoms in size, the fluorescence of nanoclusters can be tuned using DNA overhangs. In this study, we explored the properties of AgNCs manufactured on a short single-stranded (dC) 12 when adjacent G-rich sequences (dG N , with N = 3-15) were added. The 'red' emission of AgNC@dC 12 with λ MAX = 660 nm dramatically changed upon the addition of a G-rich overhang with N G = 15. The pattern of the emission-excitation matrix (EEM) suggested the emergence of two new emissive states at λ MAX = 575 nm and λ MAX = 710 nm. The appearance of these peaks provides an effective way to design biosensors capable of detecting specific nucleic acid sequences with low fluorescence backgrounds. We used this property to construct an NA-based switch that brings AgNC and the G overhang near one another, turning 'ON' the new fluorescence peaks only when a specific miRNA sequence is present. Next, we tested this detection switch on miR-371, which is overexpressed in prostate cancer. The results presented provide evidence that this novel fluorescent switch is both sensitive and specific with a limit of detection close to 22 picomoles of the target miR-371 molecule.

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Tailed‐Hoogsteen Triplex DNA Silver Nanoclusters Emit Red Fluorescence upon Target miRNA Sensing

Yadavalli,

Park,

Kim

et al. 2023

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MicroRNAs (miRNAs) are small RNA molecules, typically 21‒22 nucleotides in size, which play a crucial role in regulating gene expression in most eukaryotes. Their significance in various biological processes and disease pathogenesis has led to considerable interest in their potential as biomarkers for diagnosis and therapeutic applications. In this study, a novel method for sensing target miRNAs using Tailed‐Hoogsteen triplex DNA‐encapsulated Silver Nanoclusters (DNA/AgNCs) is introduced. Upon hybridization of a miRNA with the tail, the Tailed‐Hoogsteen triplex DNA/AgNCs exhibit a pronounced red fluorescence, effectively turning on the signal. It is successfully demonstrated that this miRNA sensor not only recognized target miRNAs in total RNA extracted from cells but also visualized target miRNAs when introduced into live cells, highlighting the advantages of the turn‐on mechanism. Furthermore, through gel‐fluorescence assays and small‐angle X‐ray scattering (SAXS) analysis, the turn‐on mechanism is elucidated, revealing that the Tailed‐Hoogsteen triplex DNA/AgNCs undergo a structural transition from a monomer to a dimer upon sensing the target miRNA. Overall, the findings suggest that Tailed‐Hoogsteen triplex DNA/AgNCs hold great promise as practical sensors for small RNAs in both in vitro and cell imaging applications.

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DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Cited by 20 publications

References 47 publications

Hg2+ Detection with Rational Design of DNA-Templated Fluorescent Silver Nanoclusters

Hg2+ Detection with Rational Design of DNA-Templated Fluorescent Silver Nanoclusters

Detection of cancer‐associated miRNA using a fluorescence switch of AgNC@NA and guanine‐rich overhang sequences

Tailed‐Hoogsteen Triplex DNA Silver Nanoclusters Emit Red Fluorescence upon Target miRNA Sensing

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