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

An Atom-Precise Understanding of DNA-Stabilized Silver Nanoclusters

ConspectusDNA-stabilized silver nanoclusters (AgN-DNAs) are sequence-encoded fluorophores. Like other noble metal nanoclusters, the optical properties of AgN-DNAs are dictated by their atomically precise sizes and shapes. What makes AgN-DNAs unique is that nanocluster size and shape are controlled by nucleobase sequence of the templating DNA oligomer. By choice of DNA sequence, it is possible to synthesize a wide range of AgN-DNAs with diverse emission colors and other intriguing photophysical properties. AgN-DNAs hold significant potential as "programmable" emitters for biological imaging due to their combination of small molecular-like sizes, bright and sequence-tuned fluorescence, low toxicities, and cost-effective synthesis. In particular, the potential to extend AgN-DNAs into the second near-infrared region (NIR-II) is promising for deep tissue imaging, which is a major area of interest for advancing biomedical imaging. Achieving this goal requires a deep understanding of the structure-property relationships that govern AgN-DNAs in order to design AgN-DNA emitters with sizes and geometries that support NIR-II emission.In recent years, major advances have been made in understanding the structure and composition of AgN-DNAs, enabling new insights into the correlation of nanocluster structure and photophysical properties. These advances have hinged on combined innovations in mass characterization and crystallography of compositionally pure AgN-DNAs, together with combinatorial experiments and machine learning-guided design. A combined approach is essential due to the major challenge of growing suitable AgN-DNA crystals for diffraction and to the labor-intensive nature of preparing and solving the molecular formulas of atomically precise AgN-DNAs by mass spectrometry. These approaches alone are not feasibly scaled to explore the large sequence space of DNA oligomer templates for AgN-DNAs.This account describes recent fundamental advances in AgN-DNA science that have been enabled by high throughput synthesis and fluorimetry together with detailed analytical studies of purified AgN-DNAs. First, short introductions to nanocluster chemistry and AgN-DNA basics are presented. Then, we review recent large-scale studies that have screened thousands of DNA templates for AgN-DNAs, leading to discovery of distinct classes of these emitters with unique cluster core compositions and ligand chemistries. In particular, the discovery of a new class of chloride-stabilized AgN-DNAs enabled the first ab initio calculations of AgN-DNA electronic structure and present new approaches to stabilize these emitters in biologically relevant conditions. Near-infrared (NIR) emissive AgN-DNAs are also found to exhibit diverse structures and properties. Finally, we conclude by highlighting recent proof-of-principle demonstrations of NIR AgN-DNAs for targeted fluorescence imaging. Continued efforts may future push AgN-DNAs into the tissue transparency window for fluorescence imaging in the NIR-II tissue transparency window.

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

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.

Demonstrating the Synthesis and Antibacterial Properties of Nanostructured Silver

Investigating and understanding novel antibacterial agents is a necessary task as there is a constant increase in the number of multidrug-resistant bacterial species. The use of nanotechnology to combat drug-resistant bacteria is an important research area. The laboratory experiment described herein demonstrates that changes in the nanostructure of a material lead to significantly different antibacterial efficacies. Silver has been known to be an effective antibacterial agent throughout history, but its therapeutic uses are limited when present as either the bulk material or cations in solution. Silver nanoparticles (AgNPs) and DNA-templated silver nanoclusters (DNA-AgNCs) are both nanostructured silver materials that show vastly different antibacterial activities when incubated with E. coli in liquid culture. This work aims to provide students with hands-on experience in the synthesis and characterization of nanomaterials and basic microbiology skills; moreover, it is applicable to undergraduate and graduate curricula.

DNA-AgNC Loaded Liposomes for Measuring Cerebral Blood Flow Using Two-Photon Fluorescence Correlation Spectroscopy

Unraveling the transport of drugs and nanocarriers in cerebrovascular networks is important for pharmacokinetic and hemodynamic studies but is challenging due to the complexity of sensing individual particles within the circulatory system of a live animal. Here, we demonstrate that a DNA-stabilized silver nanocluster (DNA-Ag16NC) that emits in the first near-infrared window upon two-photon excitation in the second NIR window can be used for multiphoton in vivo fluorescence correlation spectroscopy for the measurement of cerebral blood flow rates in live mice with high spatial and temporal resolution. To ensure bright and stable emission during in vivo experiments, we loaded DNA-Ag16NCs into liposomes, which served the dual purposes of concentrating the fluorescent label and protecting it from degradation. DNA-Ag16NC-loaded liposomes enabled the quantification of cerebral blood flow velocities within individual vessels of a living mouse.

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

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 (dGN , with N = 3-15) were added. The 'red' emission of AgNC@dC12 with λMAX  = 660 nm dramatically changed upon the addition of a G-rich overhang with NG  = 15. The pattern of the emission-excitation matrix (EEM) suggested the emergence of two new emissive states at λMAX  = 575 nm and λMAX  = 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.

Recent Advances in the DNA-Mediated Multi-Mode Analytical Methods for Biological Samples

DNA-mediated nanotechnology has become a research hot spot in recent decades and is widely used in the field of biosensing analysis due to its distinctive properties of precise programmability, easy synthesis and high stability. Multi-mode analytical methods can provide sensitive, accurate and complementary analytical information by merging two or more detection techniques with higher analytical throughput and efficiency. Currently, the development of DNA-mediated multi-mode analytical methods by integrating DNA-mediated nanotechnology with multi-mode analytical methods has been proved to be an effective assay for greatly enhancing the selectivity, sensitivity and accuracy, as well as detection throughput, for complex biological analysis. In this paper, the recent progress in the preparation of typical DNA-mediated multi-mode probes is reviewed from the aspect of deoxyribozyme, aptamer, templated-DNA and G-quadruplex-mediated strategies. Then, the advances in DNA-mediated multi-mode analytical methods for biological samples are summarized in detail. Moreover, the corresponding current applications for biomarker analysis, bioimaging analysis and biological monitoring are introduced. Finally, a proper summary is given and future prospective trends are discussed, hopefully providing useful information to the readers in this research field.

Optical, structural, and biological properties of silver nanoclusters formed within the loop of a C-12 hairpin sequence

Silver nanoclusters (AgNCs) are the next-generation nanomaterials representing supra-atomic structures where silver atoms are organized in a particular geometry. DNA can effectively template and stabilize these novel fluorescent AgNCs. Only a few atoms in size - the properties of nanoclusters can be tuned using only single nucleobase replacement of C-rich templating DNA sequences. A high degree of control over the structure of AgNC could greatly contribute to the ability to fine-tune the properties of silver nanoclusters. In this study, we explore the properties of AgNCs formed on a short DNA sequence with a C12 hairpin loop structure (AgNC@hpC12). We identify three types of cytosines based on their involvement in the stabilization of AgNCs. Computational and experimental results suggest an elongated cluster shape with 10 silver atoms. We found that the properties of the AgNCs depend on the overall structure and relative position of the silver atoms. The emission pattern of the AgNCs depends strongly on the charge distribution, while all silver atoms and some DNA bases are involved in optical transitions based on molecular orbital (MO) visualization. We also characterize the antibacterial properties of silver nanoclusters and propose a possible mechanism of action based on the interactions of AgNCs with molecular oxygen.

DNA-Templated Silver Nanoclusters as Dual-Mode Sensitive Probes for Self-Powered Biosensor Fueled by Glucose

Nanomaterials have been extensively explored in developing sensors due to their unique properties, contributing to the development of reliable sensor designs with improved sensitivity and specificity. Herein, we propose the construction of a fluorescent/electrochemical dual-mode self-powered biosensor for advanced biosensing using DNA-templated silver nanoclusters (AgNCs@DNA). AgNC@DNA, due to its small size, exhibits advantageous characteristics as an optical probe. We investigated the sensing efficacy of AgNCs@DNA as a fluorescent probe for glucose detection. Fluorescence emitted by AgNCs@DNA served as the readout signal as a response to more H₂O₂ being generated by glucose oxidase for increasing glucose levels. The second readout signal of this dual-mode biosensor was utilized via the electrochemical route, where AgNCs served as charge mediators between the glucose oxidase (GOx) enzyme and carbon working electrode during the oxidation process of glucose catalyzed by GOx. The developed biosensor features low-level limits of detection (LODs), ~23 μM for optical and ~29 μM for electrochemical readout, which are much lower than the typical glucose concentrations found in body fluids, including blood, urine, tears, and sweat. The low LODs, simultaneous utilization of different readout strategies, and self-powered design demonstrated in this study open new prospects for developing next-generation biosensor devices.

Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters

Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.

Structural Characterization of DNA-Templated Silver Nanoclusters by Energy Dispersive Spectroscopy

Here, a novel method of structural determination for DNA-templated silver nanoclusters (DNA-AgNCs) is introduced. This technique uses energy dispersive spectroscopy (EDS) coupled with a scanning electron microscope (SEM) to analyze a monodisperse solution of nucleic acid-based structures. Exploiting the consistent number of phosphate atoms in each structure, we determine the average number of silver atoms that make up the DNA-AgNCs. Proper sample preparation and fine-tuning of the SEM/EDS system settings were combined to achieve highly repeatable data.

Synthesis of DNA-Templated Silver Nanoclusters and the Characterization of Their Optical Properties and Biological Activity

DNA-templated silver nanoclusters (DNA-AgNCs) are a unique class of bioinorganic nanomaterials. The optical properties and biological activities of DNA-AgNCs are readily modulated by the minor adjustments in the sequence or structure of the templating oligonucleotide. Excitation-emission matrix spectroscopy (EEMS) enables the fluorescence of compounds to be measured in a way that examines the entirety of a material's fluorescent properties. The use of EEMS for the characterization of DNA-AgNCs allows for multiple fluorescence peaks to be readily identified while providing the excitation and emission wavelengths of each signal. To assess the antibacterial and cytotoxic activities of DNA-AgNCs, two separate experimental approaches are used. Assessing the growth of bacteria over time is accomplished by measuring the optical density of the bacterial suspension with 600 nm light, which is directly related to the number of bacteria in suspension. In order to evaluate the DNA-AgNCs for cytotoxic activity, cell viability assays which probe mitochondrial activity were used. Herein, we describe protocols for the characterization of the fluorescent, antibacterial, and cytotoxic activities of DNA-AgNCs using EEM, optical density measurements, and cell viability assays.

Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures

Molecular dynamics (MD) simulations can be used to investigate the stability and conformational characteristics of RNA nanostructures. However, MD simulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we introduce the preparation and MD simulations of two RNA kissing loop (KL) motifs, a linear KL complex and a bent KL complex, and an RNA nanoring. The initial solvated system and topology files of each system will be prepared by two major force fields, AMBER and CHARMM force fields. MD simulations will be performed by NAMD simulation package, which can accept both force fields. In addition, we will introduce the use of the AMBER cpptraj program and visual molecular dynamics (VMD) for data analysis. We will also discuss how MD simulations of two KL motifs can be used to estimate the conformation and stability of RNA nanoring as well as to explain the vibrational characteristics of RNA nanoring.

Inhibition of Bacteria In Vitro and In Vivo by Self-Assembled DNA-Silver Nanocluster Structures

Antimicrobial nanomaterials hold great promise for bacteria-infected wound healing. However, it remains a challenge to balance antimicrobial efficacy and biocompatibility for these artificial antimicrobials. Here we employed biocompatible genetic molecule DNA as a building material to fabricate antimicrobial materials, including self-assembled Y-shaped DNA-silver nanocluster composite (Y-Ag) and Y-Ag hydrogel (Y-Ag-gel). We demonstrate that macroscopic and microcosmic DNA-Ag composites can effectively inhibit bacterial growth but do not affect cell proliferation in vitro. In particular, Y-Ag spray can speed up the process of wound healing in vivo. Considering the efficacy and advantages of DNA-based materials, our findings provide a promising route to fabricate a novel wound dressing such as spray and hydrogel for therapeutic wound healing.

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

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+.