Excited-State Dynamics in a DNA-Stabilized Ag16 Cluster with Near-Infrared Emission

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.

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.

Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation

DNA-stabilized silver nanoclusters (DNA-AgNCs) are a class of fluorophores with interesting photophysical properties dominated by the choice of DNA sequence. Screening methods with ultraviolet excitation and steady state well plate readers have previously been used for deepening the understanding between DNA sequence and emission color of the resulting DNA-AgNCs. Here, we present a new method for screening DNA-AgNCs by using pulsed white light excitation (λex ≈ 490-900 nm). By subtraction and time gating we are able to circumvent the dominating scatter of the white excitation light and extract both temporally and spectrally resolved emission of DNA-AgNCs over the visible to near-infrared range. Additionally, we are able to identify weak long-lived emission, which is often buried underneath the intense nanosecond fluorescence. This new approach will be useful for future screening of DNA-AgNCs (or other novel emissive materials) and aid machine-learning models by providing a richer training data set.

On transient absorption and dual emission of the atomically precise, DNA-stabilized silver nanocluster Ag16Cl2

DNA-stabilized silver nanoclusters with 10 to 30 silver atoms are interesting biocompatible nanomaterials with intriguing fluorescence properties. However, they are not well understood, since atom-scale high level theoretical calculations have not been possible due to a lack of firm experimental structural information. Here, by using density functional theory (DFT), we study the recently atomically resolved (DNA)2-Ag16Cl2 nanocluster in solvent under the lowest-lying singlet (S1) and triplet (T1) excited states, estimate the relative emission maxima for the allowed (S1 → S0) and dark (T1 → S0) transitions, and evaluate the transient absorption spectra. Our results offer a potential interpretation of the recently reported transient absorption and dual emission of similar DNA-stabilized silver nanoclusters, providing a mechanistic view on their photophysical properties that are attractive for applications in biomedical imaging and biophotonics.

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.

Time gated Fourier transform spectroscopy with burst excitation for time-resolved spectral maps from the nano- to millisecond range

We demonstrate burst-mode Time Gated Fourier Transform Spectroscopy (bmTG-FTS), a technique for simultaneously capturing and disentangling emission signals from short- (ns) and long-lived (μs-ms) states. We showcase the possibilities of the technique by preparing time gated temporal-spectral maps from a dual-emissive DNA-stabilized silver nanocluster (DNA-AgNC).

A DNA-Stabilized Ag18 12+ Cluster with Excitation-Intensity-Dependent Dual Emission

DNA-stabilized silver nanoclusters (DNA-AgNCs) are easily tunable emitters with intriguing photophysical properties. Here, a DNA-AgNC with dual emission in the red and near-infrared (NIR) regions is presented. Mass spectrometry data showed that two DNA strands stabilize 18 silver atoms with a nanocluster charge of 12+. Besides determining the composition and charge of DNA2 [Ag18 ]12+ , steady-state and time-resolved methods were applied to characterize the picosecond red fluorescence and the relatively intense microsecond-lived NIR luminescence. During this process, the luminescence-to-fluorescence ratio was found to be excitation-intensity-dependent. This peculiar feature is very rare for molecular emitters and allows the use of DNA2 [Ag18 ]12+ as a nanoscale excitation intensity probe. For this purpose, calibration curves were constructed using three different approaches based either on steady-state or time-resolved emission measurements. The results showed that processes like thermally activated delayed fluorescence (TADF) or photon upconversion through triplet-triplet annihilation (TTA) could be excluded for DNA2 [Ag18 ]12+ . We, therefore, speculate that the ratiometric excitation intensity response could be the result of optically activated delayed fluorescence.

Bioconjugation of a Near-Infrared DNA-Stabilized Silver Nanocluster to Peptides and Human Insulin by Copper-Free Click Chemistry

DNA-stabilized silver nanoclusters (DNA-AgNCs) are biocompatible emitters with intriguing properties. However, they have not been extensively used for bioimaging applications due to the lack of structural information and hence predictable conjugation strategies. Here, a copper-free click chemistry method for linking a well-characterized DNA-AgNC to molecules of interest is presented. Three different peptides and a small protein, human insulin, were tested as labeling targets. The conjugation to the target compounds was verified by MS, HPLC, and time-resolved anisotropy measurements. Moreover, the spectroscopic properties of DNA-AgNCs were found to be unaffected by the linking reactions. For DNA-AgNC-conjugated human insulin, fluorescence imaging studies were performed on Chinese hamster ovary (CHO) cells overexpressing human insulin receptor B (hIR-B). The specific staining of the CHO cell membranes demonstrates that DNA-AgNCs are great candidates for bioimaging applications, and the proposed linking strategy is easy to implement when the DNA-AgNC structure is known.

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.