Switchable Dual-Emissive DNA-Stabilized Silver Nanoclusters

Nonradiative Deactivation of the Fluorescent Ag16-DNA and Ag10-DNA Emitters: The Role of Water

The luminescent quantum yield of silver-cluster emitters stabilized by short oligonucleotides (AgN-DNA) may be efficiently tuned by replacing nucleobases in their stabilization DNA matrices with analogues. In the present study, we proposed a valuable and straightforward theoretical methodology for assessing the photophysical behaviors emerging in AgN-DNA emitters after excitation. Using green Ag10-DNA and near-IR Ag16-DNA emitters we demonstrate how point guanine/inosine replacement could affect the photophysical rate constants of radiative/nonradiative processes. The main deactivation channel of the fluorescence of Ag16-DNA is intersystem crossing, which is in line with experimental data, whereas for Ag10-DNA the calculations overestimate the intersystem crossing rate possibly due to pure solvent contributions.

Multi-Objective Design of DNA-Stabilized Nanoclusters Using Variational Autoencoders With Automatic Feature Extraction

DNA-stabilized silver nanoclusters (AgN-DNAs) have sequence-tuned compositions and fluorescence colors. High-throughput experiments together with supervised machine learning models have recently enabled design of DNA templates that select for AgN-DNA properties, including near-infrared (NIR) emission that holds promise for deep tissue bioimaging. However, these existing models do not enable simultaneous selection of multiple AgN-DNA properties, and require significant expert input for feature engineering and class definitions. This work presents a model for multiobjective, continuous-property design of AgN-DNAs with automatic feature extraction, based on variational autoencoders (VAEs). This model is generative, i.e., it learns both the forward mapping from DNA sequence to AgN-DNA properties and the inverse mapping from properties to sequence, and is trained on an experimental data set of DNA sequences paired with AgN-DNA fluorescence properties. Experimental testing shows that the model enables effective design of AgN-DNA emission, including bright NIR AgN-DNAs with 4-fold greater abundance compared to training data. In addition, Shapley analysis is employed to discern learned nucleobase patterns that correspond to fluorescence color and brightness. This generative model can be adapted for a range of biomolecular systems with sequence-dependent properties, enabling precise design of emerging biomolecular nanomaterials.

Energy Transfer Between i-Motif DNA Encapsulated Silver Nanoclusters and Fluorescein Amidite Efficiently Visualizes the Redox State of Live Cells

The redox regulation, maintaining a balance between oxidation and reduction in living cells, is vital for cellular homeostasis, intricate signaling networks, and appropriate responses to physiological and environmental cues. Here, a novel redox sensor, based on DNA-encapsulated silver nanoclusters (DNA/AgNCs) and well-defined chemical fluorophores, effectively illustrating cellular redox states in live cells is introduced. Among various i-motif DNAs, the photophysical property of poly-cytosines (C20)-encapsulated AgNCs that sense reactive oxygen species (ROS) is adopted. However, the sensitivity of C20/AgNCs is insufficient for evaluating ROS levels in live cells. To overcome this drawback, the ROS sensing mechanism of C20/AgNCs through gel electrophoresis, mass spectrometry, and small-angle X-ray scattering is primarily defined. Then, by tethering fluorescein amidite (FAM) and Cyanine 5 (Cy5) dyes to each end of the C20/AgNCs sensor, an Energy Transfer (ET) between AgNCs and FAM is achieved, resulting in intensified green fluorescence upon ROS detection. Taken together, the FAM-C20/AgNCs-Cy5 redox sensor enables dynamic visualization of intracellular redox states, yielding insights into oxidative stress-related processes in live cells.

Analytical method for the determination of the absorption coefficient of DNA-stabilized silver nanoclusters

DNA-stabilized silver nanoclusters (DNA-AgNCs) are biocompatible emitters formed by silver atoms and cations encapsulated in DNA oligomers. Here, we present an analytical approach to calculate the molar absorption coefficient (ε) of these systems, which consists of combining UV-Vis spectroscopy, electrospray ionization-mass spectrometry (ESI-MS), and inductively coupled plasma-optical emission spectrometry (ICP-OES). ESI-MS enables the determination of the number of silvers bound to the DNA strands, whereas ICP-OES allows measurement of the total amount of silver in solution. The data is used to calculate the concentration of DNA-AgNCs and together with UV-Vis absorbance, allows for the calculation of ε. We compare the obtained ε with the experimental values previously determined through fluorescence correlation spectroscopy (FCS) and theoretical estimates based on the ε of the DNA itself. Finally, the experimental radiative decay rates (kf) and ε values are evaluated and compared to those typically found for organic fluorophores, highlighting the molecular-like nature of the DNA-AgNC emission.

Intrinsic dual emissive insulin capped Au/Ag nanoclusters as single ratiometric nanoprobe for reversible detection of pH and temperature and cell imaging

pH and temperature are two important characteristics in cells and the environment. These, not only in the well-done regulation of cell functions but also in diagnosis and treatment, have a key role. Protein-protected bimetallic nanoclusters are abundantly used in the building of biosensors. However, insulin-stabilized Au-Ag nanoclusters with dual intrinsic emission have not been investigated yet. In this work, Dual emissive insulin templated Au-Ag nanocluster (Ins(Au/Ag)NCs) were first synthesized in a simple and green one-put manner. The two emission wavelengths of, as-prepared NCs centered at 410 and 630 nm, excited in one excitation wavelength (330 nm). These two emission peaks were assigned to the di-Tyrosine cross-linked formation and bimetallic nanoclusters respectively. Further analysis displayed that each emission band of Ins(Au/Ag)NCs responded to one variable whilst another peak remained constant; For blue and red emission wavelengths, pH dependency and thermo-responsibility were observed respectively. As-prepared nanoprobe with the intrinsic dual emissive feature was used for ratiometric determination of these parameters, each with a discrete response from another. The linear range of 6.0-9.0 for pH and 1 to 71 °C for temperature was obtained, which comprises the physiological range of pH and temperature and afforded intracellular sensing and imaging capability. As-prepared NCs probe show excellent biocompatibility and cell membrane permeability, and so were successfully applied as direct ratiometric pH and temperature probes in HeLa and HFF cells. More interestingly, this dual emissive nanoprobe is capable of distinguishing cancer cells from normal ones.

A Combined Quantum Mechanics and Molecular Mechanics Approach for Simulating the Optical Properties of DNA-Stabilized Silver Nanoclusters

DNA-stabilized silver nanoclusters have emerged as an intriguing type of nanomaterial due to their unique optical and electronic properties, with potential applications in areas such as biosensing and imaging. The development of efficient methods for modeling these properties is paramount for furthering the understanding and utilization of these clusters. In this study, a hybrid quantum mechanical and molecular mechanical approach for modeling the optical properties of a DNA-templated silver nanocluster is evaluated. The influence of different parameters, including ligand fragmentation, damping, embedding potential, basis set, and density functional, is investigated. The results demonstrate that the most important parameter is the type of atomic properties used to represent the ligands, with isotropic dipole-dipole polarizabilities outperforming the rest. This underscores the importance of an appropriate representation of the ligands, particularly through the selection of the properties used to represent them. Moreover, the results are compared to experimental data, showing that the applied methodology is reliable and effective for the modeling of DNA-stabilized silver nanoclusters. These findings offer valuable insights that may guide future computational efforts to explore and harness the potential of these novel systems.

Beyond nature's base pairs: machine learning-enabled design of DNA-stabilized silver nanoclusters

Sequence-encoded biomolecules such as DNA and peptides are powerful programmable building blocks for nanomaterials. This paradigm is enabled by decades of prior research into how nucleic acid and amino acid sequences dictate biomolecular interactions. The properties of biomolecular materials can be significantly expanded with non-natural interactions, including metal ion coordination of nucleic acids and amino acids. However, these approaches present design challenges because it is often not well-understood how biomolecular sequence dictates such non-natural interactions. This Feature Article presents a case study in overcoming challenges in biomolecular materials with emerging approaches in data mining and machine learning for chemical design. We review progress in this area for a specific class of DNA-templated metal nanomaterials with complex sequence-to-property relationships: DNA-stabilized silver nanoclusters (AgN-DNAs) with bright, sequence-tuned fluorescence colors and promise for biophotonics applications. A brief overview of machine learning concepts is presented, and high-throughput experimental synthesis and characterization of AgN-DNAs are discussed. Then, recent progress in machine learning-guided design of DNA sequences that select for specific AgN-DNA fluorescence properties is reviewed. We conclude with emerging opportunities in machine learning-guided design and discovery of AgN-DNAs and other sequence-encoded biomolecular nanomaterials.

Elucidating the Mystery of DNA-Templating Effects on a Silver Nanocluster

This presentation considers the effects that DNA-templating has on the optical properties of a 16-atom silver cluster. To accomplish this, hybrid quantum mechanical and molecular mechanical simulations of a Ag₁₆-DNA complex have been carried out and compared with pure time-dependent density functional theory calculations of two Ag₁₆ clusters in vacuum. The presented results show that the templating DNA polymers both red-shift the one-photon absorption of the silver cluster and increase its intensity. This occurs through a change in cluster shape prompted by the structural constraints of the DNA ligands combined with silver-DNA interactions. The overall charge of the cluster also contributes to the observed optical response, as oxidation of the cluster results in a simultaneous blue-shift of the one-photon absorption and a decrease in intensity. Additionally, the changes in shape and environment also lead to a blue-shift and enhancement of the two-photon absorption.

CRISPR/Cas Precisely Regulated DNA-Templated Silver Nanocluster Fluorescence Sensor for Meat Adulteration Detection

Meat adulteration can cause consumer fraud, food allergies, and religious issues. Rapid and sensitive detection methods are urgently demanded to supervise meat authenticity. Herein, a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas precisely regulated DNA-templated silver nanocluster (DNA-AgNC) sensor was ingeniously designed to detect meat adulteration. Specific sequence recognition of CRISPR/Cas12a allowed accurate identification of target DNA. The emerging label-free fluorescent probes, DNA-AgNCs, a class of promising fluorophores in biochemical analysis with attractive photostability and remarkably enhanced fluorescence properties, were first introduced as the substrates of CRISPR/Cas12a system, allowing a sensitive output of amplified signals through the precise regulation of the unique target DNA-activated trans-cleavage activity of Cas12a. Based on this specific recognition, efficient signal transduction of CRISPR/Cas12a, and the outstanding fluorescence properties of DNA-AgNCs, the proposed strategy achieved a satisfactory linear range from 10 pM to 1 μM with a limit of detection (LOD) as low as 1.9 pM, which can achieve sensitive detection of meat adulteration.

Chemistry-Informed Machine Learning Enables Discovery of DNA-Stabilized Silver Nanoclusters with Near-Infrared Fluorescence

DNA can stabilize silver nanoclusters (Ag_N-DNAs) whose atomic sizes and diverse fluorescence colors are selected by nucleobase sequence. These programmable nanoclusters hold promise for sensing, bioimaging, and nanophononics. However, DNA's vast sequence space challenges the design and discovery of Ag_N-DNAs with tailored properties. In particular, Ag_N-DNAs with bright near-infrared luminescence above 800 nm remain rare, placing limits on their applications for bioimaging in the tissue transparency windows. Here, we present a design method for near-infrared emissive Ag_N-DNAs. By combining high-throughput experimentation and machine learning with fundamental information from Ag_N-DNA crystal structures, we distill the salient DNA sequence features that determine Ag_N-DNA color, for the entire known spectral range of these nanoclusters. A succinct set of nucleobase staple features are predictive of Ag_N-DNA color. By representing DNA sequences in terms of these motifs, our machine learning models increase the design success for near-infrared emissive Ag_N-DNAs by 12.3 times as compared to training data, nearly doubling the number of known Ag_N-DNAs with bright near-infrared luminescence above 800 nm. These results demonstrate how incorporating known structure-property relationships into machine learning models can enhance materials study and design, even for sparse and imbalanced training data.

Silver Nanoclusters Serve as Fluorescent Rivets Linking Hoogsteen Triplex DNA and Hairpin-Loop DNA Structures

Greater understanding of the mutual influence between DNA and the associated nanomaterial on the properties of each other can provide alternative strategies for designing and developing DNA nanomachines. DNA secondary structures are essential for encapsulating highly emissive silver nanoclusters (DNA/AgNCs). Likewise, AgNCs stabilize secondary DNA structures, such as hairpin DNA, duplex DNA, and parallel-motif DNA triplex. In this study, we found that the fluorescence of AgNCs encapsulated within a Hoogsteen triplex DNA structure can be turned on and off in response to pH changes. We also show that AgNCs can act as nanoscale rivets, linking two functionally distinctive DNA nanostructures. For instance, we found that a Hoogsteen triplex DNA structure with a seven-cytosine loop encapsulates red fluorescent AgNCs. The red fluorescence faded under alkaline conditions, whereas the fluorescence was restored in a near-neutral environment. Hairpin DNA and random DNA structures did not exhibit this pH-dependent AgNCs fluorescence. A fluorescence lifetime measurement and a small-angle X-ray scattering analysis showed that the triplex DNA-encapsulated AgNCs were photophysically convertible between bright and dark states. An in-gel electrophoresis analysis indicated that bright and dark convertibility depended on the AgNCs-riveted dimerization of the triplex DNAs. Moreover, we found that AgNCs rivet the triplex DNA and hairpin DNA to form a heterodimer, emitting orange fluorescence. Our findings suggest that AgNCs between two cytosine-rich loops can be used as nanorivets in designing noncanonical DNA origami beyond Watson-Crick base pairing.

Detection of inflammatory bowel disease (IBD)-associated microRNAs by two color DNA-templated silver nanoclusters fluorescent probes

Researches demonstrated that circulating miRNAs could be used as novel diagnostic and prognostic potential markers for patients with inflammatory bowel diseases (IBD). It is of great significance in clinical to develop rapid and specific detection methods for miRNAs. Herein, we established a fluorescent probe for ulcerative colitis (UC) activity-associated two serum biomarkers (miR-23a and miR-223) simultaneous detection, which used multi-color fluorescent DNA-stabilized silver nanoclusters (DNA-AgNC) illuminated by a close guanine (G)-rich sequence as a signal transducer and two split DNA probes as recognition units. In principle, the two DNA probe sequences containing AgNC nucleation sequence and G-rich sequence respectively, formed a ternary complex when in the presence of target miRNA through base pairing, so as to induce enhancement of fluorescence emission of AgNC by shortening the distance from G-rich sequence. The combined probes for miR-23a and miR-223 detection generated increased fluorescence signals at 460 nm ex/545 nm em and at 560 nm ex/630 nm em, respectively. With this technique, we successfully quantified the two target miRNAs with high selectivity. Furthermore, the potential clinic applicability of this method was verified by testing the spiked standard miRNAs in human serum. Thus, this one-step, low-cost, and homogenous method offers a great opportunity for disease-associated multiplex miRNAs simultaneous detection.

Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores

Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag⁺-nucleobase base pairs, and Ag⁰ chromophores. The DNA host C₄-A₂-iC₄T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C₄-A₂-iC₄T)₂/Ag₁₁⁷⁺ with λ_abs/λ_em = 430/520 nm and (C₄-A₂-iC₄T)₂/Ag₁₄⁸⁺ with λ_abs/λ_em = 510/630 nm. The Ag⁺ and Ag⁰ constituents in these partially oxidized clusters are linked with structural elements in C₄-A₂-iC₄T. Ag⁺ alone binds sparsely but strongly to form C₄-A₂-iC₄T/3-4 Ag⁺ and (C₄-A₂-iC₄T)₂/7-8 Ag⁺ complexes, and these stoichiometries suggest that Ag⁺ cross-links pairs of cytosines to form a hairpin with a metallo-C₄/iC₄ duplex and an adenine loop. The Ag⁰ are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag⁺-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag⁺ disperses with the cytosines to create an adenine binding pocket for the Ag⁰ cluster chromophores.

Synthesis of Fluorescent Titanium Nanoclusters at ambient temperature for highly sensitive and selective detection of Creatine Kinase MM in myocardial infarction

Fluorescent-based biosensing in Photoluminescence nanomaterials has emerged as a new sensing platform commonly used for disease diagnosis. However, the synthesis of Titanium nanoclusters is highly challenging since Titanium is easily oxidized into TiO₂ at ambient temperature. To overcome this problem, we used an acidic medium and simple and robust protocol to synthesize the Titanium nanoclusters of 3-4 nm diameter, which could report the first fluorescent Titanium nanoclusters. New approaches for the novel synthesis of TiNCs can be used for rapid sensing of myocardial infarction (cardiac arrest). In converting creatine to phosphocreatine, CK-MM activates the reaction to convert ATP to ADP, thereby releasing the phosphate groups. Titanium nanoclusters bind strongly to the phosphate group and then quench the Fluorescence. Thus, this phenomenon can be further applied for quantification approaches. The quenching of fluorescence intensity with CK-MM concentration is linear with R² = 0.9829. The current approach can be applied for CK-MM sensing for a wide concentration range (0.625 U/L - 10 U/L). The detection limit was 0.2513 ng/ml in aqueous medium and 0.3465 ng/ml in human serum with high sensitivity when compared with the previous reported methods. Also, this is the first fluorescent-based sensing method to detect CK- MM. The fluorescent TiNCs is a novel platform to be widely applied for the phosphopeptide and phosphoprotein analysis due to the strong and covalent bondings between Ti with P atoms in the near future in medicine, biomedicine, and biological fields.

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

Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.

Observation of microsecond luminescence while studying two DNA-stabilized silver nanoclusters emitting in the 800-900 nm range

We investigated two DNA-stabilized silver nanoclusters (DNA-AgNCs) that show multiple absorption features in the visible region, and emit around 811 nm (DNA811-AgNC) and 841 nm (DNA841-AgNC). Both DNA-AgNCs have large Stokes shifts and can be efficiently excited with red light. A comparison with the commercially available Atto740 yielded fluorescence quantum yields in the same order of magnitude, but a higher photon output above 800 nm since both DNA-AgNCs are more red-shifted. The study of both DNA-AgNCs also revealed previously unobserved photophysical behavior for this class of emitters. The fluorescence quantum yield and decay time of DNA841-AgNC can be increased upon consecutive heating/cooling cycles. DNA811-AgNC has an additional absorption band around 470 nm, which is parallel in orientation to the lowest energy transition at 640 nm. Furthermore, we observed for the first time a DNA-AgNC population (as part of the DNA811-AgNC sample) with green and near-infrared emissive states with nanosecond and microsecond decay times, respectively. A similar dual emissive DNA-AgNC stabilized by a different 10-base DNA strand is also reported in the manuscript. These two examples highlight the need to investigate the presence of red-shifted microsecond emission for this class of emitters.

Structure and luminescence of DNA-templated silver clusters

DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure-property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.

Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters

DNA-stabilized silver clusters (AgN-DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of AgN-DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most AgN-DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of AgN-DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 AgN-DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive AgN-DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects AgN-DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in AgN-DNAs, and discuss how differences in AgN-DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in AgN-DNAs and the relations of this process to AgN-DNA structure.

Single-Molecule Detection of DNA-Stabilized Silver Nanoclusters Emitting at the NIR I/II Border

The near-infrared (NIR) I and II regions are known for having good light transparency of tissue and less scatter compared to the visible region of the electromagnetic spectrum. However, the number of bright fluorophores in these regions is limited. Here we present a detailed spectroscopic characterization of a DNA-stabilized silver nanocluster (DNA-AgNC) that emits at around 960 nm in solution. The DNA-AgNC converts to blue-shifted emitters over time. Embedding these DNA-AgNCs in poly(vinyl alcohol) (PVA) shows that they are bright and photostable enough to be detected at the single-molecule level. Photon antibunching experiments were performed to confirm single emitter behavior. Our findings highlight that the screening and exploration of DNA-AgNCs in the NIR II region might yield promising bright, photostable emitters that could help develop bioimaging applications with unprecedented signal-to-background ratios and single-molecule sensitivity.

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

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.

Tuning properties of silver nanoclusters with RNA nanoring assemblies

Combining atomically resolved DNA-templated silver nanoclusters (AgNCs) with nucleic acid nanotechnology opens new exciting possibilities for engineering bioinorganic nanomaterials with uniquely tunable properties. In this unforeseen cooperation, nucleic acids not only drive the formation of AgNCs but also promote their spatial organization in supra-assemblies. In this work, we confirm the feasibility of this approach using programmable RNA rings to control formation and optical properteis of six individual AgNCs. "Red" (λEXC/λEM = 565/623 nm) and "green" (λEXC/λEM = 440/523 nm) emitting AgNCs are templated on cytosine-rich DNA fragments embedded into the RNA rings. Optical properties of the AgNCs formed on the RNA rings are characterized in detail. While all "red" species passively transition to "green" emitters with time, the initial fluorescent properties and relative stabilities of "red" AgNCs can be regulated by altering the relative orientation of AgNCs within the RNA rings. As such, the oxidative stability increases dramatically for AgNC positioned towards the center of the RNA rings rather than facing outward. Overall, our findings expand the existing AgNC fluorescent toolkit while uncovering the complexity of the AgNC electronic structures with the abundance of possibilities for controlling de-excitation processes.

Micro RNA Sensing with Green Emitting Silver Nanoclusters

Micro RNA (miR) are regulatory non-coding RNA molecules, which contain a small number of nucleotides ~18-28 nt. There are many various miR sequences found in plants and animals that perform important functions in developmental, metabolic, and disease processes. miRs can bind to complementary sequences within mRNA molecules thus silencing mRNA. Other functions include cardiovascular and neural development, stem cell differentiation, apoptosis, and tumors. In tumors, some miRs can function as oncogenes, others as tumor suppressors. Levels of certain miR molecules reflect cellular events, both normal and pathological. Therefore, miR molecules can be used as biomarkers for disease diagnosis and prognosis. One of these promising molecules is miR-21, which can serve as a biomarker with high potential for early diagnosis of various types of cancer. Here, we present a novel design of miR detection and demonstrate its efficacy on miR-21. The design employs emissive properties of DNA-silver nanoclusters (DNA/AgNC). The detection probe is designed as a hairpin DNA structure with one side of the stem complimentary to miR molecule. The binding of target miR-21 opens the hairpin structure, dramatically modulating emissive properties of AgNC hosted by the C12 loop of the hairpin. "Red" fluorescence of the DNA/AgNC probe is diminished in the presence of the target miR. At the same time, "green" fluorescence is activated and its intensity increases several-fold. The increase in intensity of "green" fluorescence is strong enough to detect the presence of miR-21. The intensity change follows the concentration dependence of the target miR present in a sample, which provides the basis of developing a new, simple probe for miR detection. The detection strategy is specific, as demonstrated using the response of the DNA/AgNC probe towards the scrambled miR-21 sequence and miR-25 molecule. Additionally, the design reported here is very sensitive with an estimated detection limit at ~1 picomole of miR-21.

Unusually large fluorescence quantum yield for a near-infrared emitting DNA-stabilized silver nanocluster

Silver nanoclusters stabilized by 5′-CCCGGAGAAG-3′ DNA strands display an unusually high fluorescence quantum yield in the near-infrared region.

Targeted DNA-driven catalytic assembly light-up ratiometric fluorescence of biemissive silver nanoclusters for amplified biosensing

We report a ratiometric fluorescence strategy using biemissive silver nanoclusters that are harbored in a functional hairpin beacon for rapid, specific and sensitive detection of specific HIV-related DNA as a model.

Collective Response in DNA-Stabilized Silver Cluster Assemblies from First-Principles Simulations

We investigate fluorescence resonant energy transfer and concurrent electron dynamics in a pair of DNA-stabilized silver clusters. For this purpose we introduce a methodology for the simulation of collective optoelectronic properties of coupled molecular aggregates starting from first-principles quantum chemistry, which can be further applied to a broad range of coupled molecular systems to study their electro-optical response. Our simulations reveal the existence of low-energy coupled excitonic states, which enable ultrafast energy transport between subunits, and give insight into the origin of the fluorescence signal in coupled DNA-stabilized silver clusters, which have been recently experimentally detected. Hence, we demonstrate the possibility of constructing ultrasmall energy transmission lines and optical converters based on these hybrid molecular systems.

The effect of pH and ionic strength on the fluorescence properties of a red emissive DNA-stabilized silver nanocluster

DNA-stabilized silver nanoclusters (DNA-AgNCs) are a class of promising fluorophores for imaging and sensing applications. All aspects of their spectroscopic properties are not yet fully characterized, leaving this field still with a number of fundamental studies to be addressed. In this work, we studied the spectroscopic properties of red-emitting DNA-AgNCs at different pH (5 to 9) and ionic strength μ (0.005 to 0.5). The photophysical properties of high performance liquid chromatography (HPLC) purified DNA-AgNCs proved to be constant over a large range of pH and μ, with absorption, emission and fluorescence decay times only being affected at very high pH and μ values. Non-purified DNA-AgNCs were also unaffected by pH and/or μ variations, but significant differences can be observed between the rotational correlation times of purified and non-purified DNA-AgNCs.

Preparation and characterization of solid DNA silver nanoclusters with superior aerobic and thermal stability

In the current study, we present a universal method to preserve DNA-templated silver nanoclusters (DNA AgNCs) in the solid-state. Our results show that DNA AgNCs must be precipitated before drying. By drying the ethanol precipitated DNA AgNCs, we have successfully prepared solid DNA AgNCs with superior stability in aerobic and high-temperature environments. Although the fluorescence lifetime measurements show that the emission of DNA AgNCs is drastically quenched in the solid-state, the emission can be fully recovered in solution. To our knowledge, this is the first attempt to prepare DNA AgNCs in solid-state, and this finding provides an ideal solution for the transportation and long-term preservation of DNA AgNCs.

The solid DNA AgNCs exhibit superior stability and the fluorescence can be recovered in solution.