Probing emission of a DNA-stabilized silver nanocluster from the sub-nanosecond to millisecond timescale in a single measurement

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.

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.

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.

Interrupted DNA and Slow Silver Cluster Luminescence

A DNA-silver cluster conjugate is a hierarchical chromophore with a partly reduced silver core embedded within the DNA nucleobases that are covalently linked by the phosphodiester backbone. Specific sites within a polymeric DNA can be targeted to spectrally tune the silver cluster. Here, the repeated (C₂A)₆ strand is interrupted with a thymine, and the resulting (C₂A)₂-T-(C₂A)₄ forms only Ag₁₀⁶⁺, a chromophore with both prompt (∼1 ns) green and sustained (∼10² μs) red luminescence. Thymine is an inert placeholder that can be removed, and the two fragments (C₂A)₂ and (C₂A)₄ also produce the same Ag₁₀⁶⁺ adduct. In relation to (C₂A)₂T(C₂A)₄, the (C₂A)₂ + (C₂A)₄ pair is distinguished because the red Ag₁₀⁶⁺ luminescence is ∼6× lower, relaxes ∼30% faster, and is quenched ∼2× faster with O₂. These differences suggest that a specific break in the phosphodiester backbone can regulate how a contiguous vs broken scaffold wraps and better protects its cluster adduct.

Chloride Ligands on DNA-Stabilized Silver Nanoclusters

DNA-stabilized silver nanoclusters (Ag_N-DNAs) are known to have one or two DNA oligomer ligands per nanocluster. Here, we present the first evidence that Ag_N-DNA species can possess additional chloride ligands that lead to increased stability in biologically relevant concentrations of chloride. Mass spectrometry of five chromatographically isolated near-infrared (NIR)-emissive Ag_N-DNA species with previously reported X-ray crystal structures determines their molecular formulas to be (DNA)₂[Ag₁₆Cl₂]⁸⁺. Chloride ligands can be exchanged for bromides, which red-shift the optical spectra of these emitters. Density functional theory (DFT) calculations of the 6-electron nanocluster show that the two newly identified chloride ligands were previously assigned as low-occupancy silvers by X-ray crystallography. DFT also confirms the stability of chloride in the crystallographic structure, yields qualitative agreement between computed and measured UV-vis absorption spectra, and provides interpretation of the ³⁵Cl-nuclear magnetic resonance spectrum of (DNA)₂[Ag₁₆Cl₂]⁸⁺. A reanalysis of the X-ray crystal structure confirms that the two previously assigned low-occupancy silvers are, in fact, chlorides, yielding (DNA)₂[Ag₁₆Cl₂]⁸⁺. Using the unusual stability of (DNA)₂[Ag₁₆Cl₂]⁸⁺ in biologically relevant saline solutions as a possible indicator of other chloride-containing Ag_N-DNAs, we identified an additional Ag_N-DNA with a chloride ligand by high-throughput screening. Inclusion of chlorides on Ag_N-DNAs presents a promising new route to expand the diversity of Ag_N-DNA structure-property relationships and to imbue these emitters with favorable stability for biophotonics applications.

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

Due to desirable optical properties, such as efficient luminescence and large Stokes shift, DNA-templated silver nanoclusters (DNA-AgNCs) have received significant attention over the past decade. Nevertheless, the excited-state dynamics of these systems are poorly understood, as studies of the processes ultimately leading to a fluorescent state are scarce. Here we investigate the early time relaxation dynamics of a 16-atom silver cluster (DNA-Ag₁₆NC) featuring NIR emission in combination with an unusually large Stokes shift of over 5000 cm^-1. We follow the photoinduced dynamics of DNA-Ag₁₆NC on time ranges from tens of femtoseconds to nanoseconds using a combination of ultrafast optical spectroscopies, and extract a kinetic model to clarify the physical picture of the photoinduced dynamics. We expect the obtained model to contribute to guiding research efforts toward elucidating the electronic structure and dynamics of these novel objects and their potential applications in fluorescence-based labeling, imaging, and sensing.

DNA Stabilizes Eight-Electron Superatom Silver Nanoclusters with Broadband Downconversion and Microsecond-Lived Luminescence

DNA oligomers are known to serve as stabilizing ligands for silver nanoclusters (Ag_N-DNAs) with rod-like nanocluster geometries and nanosecond-lived fluorescence. Here, we report two Ag_N-DNAs that possess distinctly different structural properties and are the first to exhibit only microsecond-lived luminescence. These emitters are characterized by significant broadband downconversion from the ultraviolet/visible to the near-infrared region. Circular dichroism spectroscopy shows that the structures of these two Ag_N-DNAs differ significantly from previously reported Ag_N-DNAs. We find that these nanoclusters contain eight valence electrons, making them the first reported DNA-stabilized luminescent quasi-spherical superatoms. This work demonstrates the important role that nanocluster composition and geometry play in dictating luminescence properties of Ag_N-DNAs and significantly expands the space of structure-property relations that can be achieved for Ag_N-DNAs.

The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster

The effect of replacing guanosines with inosines in the two stabilizing strands (5'-CACCTAGCGA-3') of the NIR emissive DNA-Ag₁₆NC was investigated. The spectroscopic behavior of the inosine mutants is position-dependent: when the guanosine in position 7 was exchanged, the nanosecond fluorescence decay time shortened, while having the inosine in position 9 made the decay time longer. Thanks to structural information gained from single crystal X-ray diffraction measurements, it was possible to propose a mechanistic origin for the observed changes.