Probing heterogeneity of NIR induced secondary fluorescence from DNA-stabilized silver nanoclusters at the single molecule level

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.

Electron count and ligand composition influence the optical and chiroptical signatures of far-red and NIR-emissive DNA-stabilized silver nanoclusters

Near-infrared (NIR) emissive DNA-stabilized silver nanoclusters (AgN-DNAs) are promising fluorophores in the biological tissue transparency windows. Hundreds of NIR-emissive AgN-DNAs have recently been discovered, but their structure-property relationships remain poorly understood. Here, we investigate 19 different far-red and NIR emissive AgN-DNA species stabilized by 10-base DNA templates, including well-studied emitters whose compositions and chiroptical properties have never been reported before. The molecular formula of each purified species is determined by high-resolution mass spectrometry and correlated to its optical absorbance, emission, and circular dichroism (CD) spectra. We find that there are four distinct compositions for AgN-DNAs emissive at the far red/NIR spectral border. These emitters are either 8-electron clusters stabilized by two DNA oligomer copies or 6-electron clusters with one of three different ligand compositions: two oligomer copies, three oligomer copies, or two oligomer copies with additional chlorido ligands. Distinct optical and chiroptical signatures of 6-electron AgN-DNAs correlate with each ligand composition. AgN-DNAs with three oligomer ligands exhibit shorter Stokes shifts than AgN-DNAs with two oligomers, and AgN-DNAs with chlorido ligands have increased Stokes shifts and significantly suppressed visible CD transitions. Nanocluster electron count also significantly influences electronic structure and optical properties, with 6-electron and 8-electron AgN-DNAs exhibiting distinct absorbance and CD spectral features. This study shows that the optical and chiroptical properties of NIR-emissive AgN-DNAs are highly sensitive to nanocluster composition and illustrates the diversity of structure-property relationships for NIR-emissive AgN-DNAs, which could be harnessed to precisely tune these emitters for bioimaging applications.

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.

Sequential Two-Photon Delayed Fluorescence Anisotropy for Macromolecular Size Determination

Time-resolved fluorescence anisotropy (FA) uses the fluorophore depolarization rate to report on rotational diffusion, conformation changes, and intermolecular interactions in solution. Although FA is a rapid, sensitive, and nondestructive tool for biomolecular interaction studies, the short (∼ns) fluorescence lifetime of typical dyes largely prevents the application of FA on larger macromolecular species and complexes. By using triplet shelving and recovery of optical excitation, we introduce optically activated delayed fluorescence anisotropy (OADFA) measurements using sequential two-photon excitation, effectively stretching fluorescence anisotropy measurement times from the nanosecond scale to hundreds of microseconds. We demonstrate this scheme for measuring slow depolarization processes of large macromolecular complexes, derive a quantitative rate model, and perform Monte Carlo simulations to describe the depolarization process of OADFA at the molecular level. This setup has great potential to enable future biomacromolecular and colloidal studies.

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

A method for measuring emission over a range of sub-nanosecond to millisecond timescales is presented and demonstrated for a DNA-stabilized silver nanocluster (DNA-AgNC) displaying dual emission. This approach allows one to disentangle the temporal evolution of the two spectrally overlapping signals and to determine both the nano- and microsecond decay times of the two emission components, together with the time they take to reach the steady-state equilibrium. Addition of a second near-infrared laser, synchronized with a fixed delay, enables simultaneous characterization of optically activated delayed fluorescence (OADF). For this particular DNA-AgNC, we demonstrate that the microsecond decay times of the luminescent state and the OADF-responsible state are similar, indicating that the OADF process starts from the luminescent state.

A method for measuring emission over a range of sub-nanosecond to millisecond timescales is presented and demonstrated for a DNA-stabilized silver nanocluster (DNA-AgNC) displaying dual emission.

The effect of deuterium on the photophysical properties of DNA-stabilized silver nanoclusters

We investigated the effect of using D₂O versus H₂O as solvent on the spectroscopic properties of two NIR emissive DNA-stabilized silver nanoclusters (DNA–AgNCs). The two DNA–AgNCs were chosen because they emit in the same energy range as the third overtone of the O–H stretch. Opposite effects on the ns-lived decay were observed for the two DNA–AgNCs. Surprisingly, for one DNA–AgNC, D₂O shortened the ns decay time and enhanced the amount of µs-lived emission. We hypothesize that the observed effects originate from the differences in the hydrogen bonding strength and vibrational frequencies in the two diverse solvents. For the other DNA–AgNC, D₂O lengthened the ns decay time and made the fluorescence quantum yield approach unity at 5 °C.

We investigated the effect of using D₂O versus H₂O as solvent on the spectroscopic properties of two NIR emissive DNA-stabilized silver nanoclusters (DNA–AgNCs).

Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering

Modulating fluorescent protein emission holds great potential for increasing readout sensitivity for applications in biological imaging and detection. Here, we identify and engineer optically modulated yellow fluorescent proteins (EYFP, originally 10C, but renamed EYFP later, and mVenus) to yield new emitters with distinct modulation profiles and unique, optically gated, delayed fluorescence. The parent YFPs are individually modulatable through secondary illumination, depopulating a long-lived dark state to dynamically increase fluorescence. A single point mutation introduced near the chromophore in each of these YFPs provides access to a second, even longer-lived modulatable dark state, while a different double mutant renders EYFP unmodulatable. The naturally occurring dark state in the parent YFPs yields strong fluorescence modulation upon long-wavelength-induced dark state depopulation, allowing selective detection at the frequency at which the long wavelength secondary laser is intensity modulated. Distinct from photoswitches, however, this near IR secondary coexcitation repumps the emissive S₁ level from the long-lived triplet state, resulting in optically activated delayed fluorescence (OADF). This OADF results from secondary laser-induced, reverse intersystem crossing (RISC), producing additional nanosecond-lived, visible fluorescence that is delayed by many microseconds after the primary excitation has turned off. Mutation of the parent chromophore environment opens an additional modulation pathway that avoids the OADF-producing triplet state, resulting in a second, much longer-lived, modulatable dark state. These Optically Modulated and Optically Activated Delayed Fluorescent Proteins (OMFPs and OADFPs) are thus excellent for background- and reference-free, high sensitivity cellular imaging, but time-gated OADF offers a second modality for true background-free detection. Our combined structural and spectroscopic data not only gives additional mechanistic details for designing optically modulated fluorescent proteins but also provides the opportunity to distinguish similarly emitting OMFPs through OADF and through their unique modulation spectra.

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.

Triplet Shelving in Fluorescein and Its Derivatives Provides Delayed, Background-Free Fluorescence Detection

Fluorescence from the xanthene dyes rose bengal, erythrosine B, eosin Y, and fluorescein is modulated by reversibly optically populating and depopulating their long-lived triplet states through coillumination with a second, long-wavelength laser. Here, we show that repumping the S₁ state from the triplet generates strong, nanosecond-lived optically activated delayed fluorescence (OADF), microseconds to milliseconds after primary pulsed excitation. This time-delayed emission upon long-wavelength illumination generates fluorescence after triplet shelving and is a major contribution to fluorescence enhancement/modulation. The time-delayed and background-free OADF component is further increased using a >1 μs burst continuous wave excitation scheme to increase the steady-state triplet populations, yielding strong OADF even from strongly emissive fluorescein. Because emission is delayed long after the high-energy primary excitation, yellow-orange fluorescence is readily observed on zero background. As OADF generation depends on the triplet quantum yields and the reverse intersystem crossing rates, we directly probe the usually difficult-to-measure photophysics, create new zero-background detection schemes, and increase OADF through tailored excitation schemes, all improving sensitivity. The excellent match between experiments and simulations demonstrates the promise of these studies for OADF characterization, while enabling us to determine that OADF (in contrast to ground-state recovery and re-excitation) is the major component of fluorescence enhancement for xanthenes studied with triplet quantum yields exceeding 0.1.

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.

Disentangling optically activated delayed fluorescence and upconversion fluorescence in DNA stabilized silver nanoclusters

Optically activated delayed fluorescence (OADF) is a powerful tool for generating background-free, anti-Stokes fluorescence microscopy modalities. Recent findings, using DNA-stabilized silver nanoclusters (DNA-AgNCs), indicate that OADF is usually accompanied by a dark state-mediated consecutive photon absorption process leading to upconversion fluorescence (UCF). In this study, we disentangle the OADF and UCF process by means of wavelength-dependent NIR excitation spectroscopy. We demonstrate that, by appropriate choice of secondary NIR excitation wavelength, the dark state population can be preferentially depleted through OADF, minimizing the UCF contribution. These findings show that dark state depletion by OADF might enable background-free STED-like nanoscopy.

Optically Activated Delayed Fluorescence through Control of Cyanine Dye Photophysics

Merocyanine 540 fluorescence can be enhanced by optically depopulating dark photoisomer states to regenerate the fluorescence-generating manifold of the all-trans isomer. Here, we utilize a competing modulation route, long-wavelength coexcitation of the trans triplet population to not only modulate fluorescence through enhanced ground-state recovery but also generate optically activated delayed fluorescence (OADF) with longer-wavelength co-illumination. Such OADF (∼580 nm) is directly observed with pulsed fluorescence excitation at 532 nm, followed by long-wavelength (637 nm) continuous wave depopulation of the photogenerated triplet by repopulating the emissive S₁ state. Such reverse intersystem crossing (RISC) results in ns-lived fluorescence delayed by several microseconds after the initial primary excitation pulse and the prompt 1 ns-lived fluorescence that it induces. The dark state from which OADF is generated decays more rapidly with increased secondary laser intensity, as the optically induced RISC rate increases. This first OADF from organic dyes is observed, as the red secondary laser excites ∼580 nm, <1 ns-lived fluorescence from the previously optically prepared ∼1 μs-lived triplet state. This sequential two-photon, repumped fluorescence yields background-free collection with potential for new high-sensitivity fluorescence imaging schemes.