Free Fluorophore Research Articles

Targeted imaging of lysosomal zinc ions with a tetrahedral DNA framework fluorescent reporter.

Abnormal levels of zinc ions within endo-lysosomes have been implicated in the progression of Alzheimer's disease (AD), yet the detection of low-concentration zinc ions at the organelle level remains challenging. Here we report the design of an endo-lysosome-targeted fluorescent reporter, Znluorly, for imaging endogenous zinc ions. Znluorly is constructed from an amphiphilic DNA framework (DNF) with programmable size and shape, which can encapsulate zinc-responsive fluorophores within its hydrophobic nanocavity. We find that the tetrahedral DNFs of 20 bp in the edge length are effectively located within endo-lysosomes, which can detect zinc ions with a detection limit of ∼31.9nM (a sensitivity that is ∼2.5 times that of the free fluorophore). Given the organelle-targeting ability and high zinc sensitivity of Znluorly, we employ it to detect endogenous endo-lysosomal zinc ions in neuron cells. We monitor the dynamics of zinc levels in AD model cells and zebrafish, corroborating the positive correlation between zinc levels and AD hallmarks including Aβ aggregates and learning/memory impairments. Our study provides a generalizable strategy for organelle-specific theranostic applications.

In vivo fluorescence imaging of nanocarriers in near-infrared window II based on aggregation-caused quenching

Accurate fluorescence imaging of nanocarriers in vivo remains a challenge owing to interference derived mainly from biological tissues and free probes. To address both issues, the current study explored fluorophores in the near-infrared (NIR)-II window with aggregation-caused quenching (ACQ) properties to improve imaging accuracy. Candidate fluorophores with NIR-II emission, ACQ984 (λem = 984 nm) and IR-1060 (λem = 1060 nm), from the aza-BODIPY and cyanine families, respectively, were compared with the commercial fluorophore ICG with NIR-II tail emission and the NIR-I fluorophore P2 from the aza-BODIPY family. ACQ984 demonstrates high water sensitivity with complete fluorescence quenching at a water fraction greater than 50%. Physically embedding the fluorophores illuminates various nanocarriers, while free fluorophores cause negligible interference owing to the ACQ effect. Imaging based on ACQ984 revealed fine structures in the vascular system at high resolution. Moreover, good in vivo and ex vivo correlations in the monitoring of blood nanocarriers can be established, enabling real-time noninvasive in situ investigation of blood pharmacokinetics and dynamic distribution in various tissues. IR-1060 also has a good ACQ effect, but the lack of sufficient photostability and steady post-labeling fluorescence undermines its potential for nanocarrier bioimaging. P2 has an excellent ACQ effect, but its NIR-I emission only provides nondiscriminative ambiguous images. The failure of the non-ACQ probe ICG to display the biodistribution details serves as counterevidence for the improved imaging accuracy by NIR-II ACQ probes. Taken together, it is concluded that fluorescence imaging of nanocarriers based on NIR-II ACQ probes enables accurate in vivo bioimaging and real-time in situ pharmacokinetic analysis.

Liquid chromatography methods as a solution to inaccuracies associated with purity assessment of citric acid-based carbon dots

Herein, several analytical techniques aimed on validation of separation effectiveness of free molecular fluorophores from citric acid-based carbon dots were elaborated and compared. Generally, chromatographic methods were found more reliable than steady-state optical measurements, pointing at the LC-FLD (liquid chromatography coupled to fluorescence detector) protocols as the most sensitive. Furthermore, the applicability of the frequently reported 1H NMR technique for confirmation of the absence of highly fluorescent free low-molecular weight species in carbon dots samples was called into question. It was found that, in the case of effectively PL emitting compounds (such as 5-oxo-2,3- dihydro-5H-[1,3]thiazolo[3,2-a]pyridine-3,7-dicarboxylic acid (TPA)), the lowest concentration that could be detected with above technique (0.08 mg mL−1 of TPA) is higher than the concentration at which the particular fluorophore shows the brightest PL emission (∼0.01 mg mL−1 of TPA).

Utilising a 1,8-naphthalimide probe for the ratiometric fluorescent visualisation of caspase-3.

The development of selective and sensitive probes for monitoring caspase-3 activity-a critical enzyme involved in apoptosis-remains an area of significant interest in biomedical research. Herein, we report the synthesis and characterisation of a novel ratiometric fluorescent probe, Ac-DEVD-PABC-Naph, designed to detect caspase-3 activity. The probe utilises a 1,8-naphthalimide fluorophore covalently linked to a peptide sequence via a self-immolative p-aminobenzyl alcohol (PABA) linker. Upon enzymatic cleavage by caspase-3, the probe undergoes spontaneous degradation, releasing the free naphthalimide fluorophore, resulting in a ratiometric change in fluorescence emission. Spectroscopic studies revealed a time-dependent ratiometric fluorescent response, demonstrating the probe's ability to visualise caspase-3 activity with high sensitivity. Enzyme kinetics such as K m (Michaelis constant), k cat (turnover number), and LOD (Limit of Detection) were obtained, suggesting that the probe possesses comparable kinetic data to other probes in literature, but with the added benefits of ratiometric detection. Selectivity studies also demonstrated the probe's specificity for caspase-3 over other endogenous species and enzymes. Ac-DEVD-PABC-Naph may be a promising tool for the quantitative detection and fluorescent visualisation of caspase-3 activity in biological systems, with potential applications in apoptosis research and drug development.

Fluorescent aptasensors for sensitive detection of lead ions based on structure-switching DNA beacon probe and exonuclease I-mediated signal amplification

Herein, two simple fluorescent signal-on sensing strategies for detecting lead ions (Pb2+) were established based on structure-switching aptamer probes and exonuclease-assisted signal amplification strategies. Two hairpin-structure fluorescent probes with blunt-ended stem arms were designed by extending the base sequence of Pb2+ aptamer (PS2.M) and labelling the probes with FAM (in probe 1) and 2-aminopurine (2-AP) (in probe 2), respectively. In method 1, graphene oxide (GO) was added to adsorb probe 1 and quench the fluorescence emission of FAM to achieve low fluorescent background. In method 2, fluorescent 2-AP molecule inserted into the double-stranded DNA of probe 2 was quenched as a result of base stacking interactions, leading to a simplified, quencher-free approach. The addition of Pb2+ can induce the probes to transform into G-quadruplex structures, exposing single DNA strands at the 3′ end (the extended sequences). This exposure enables the activation of exonuclease I (Exo I) on the probes, leading to the cleavage effect and subsequent release of free bases and fluorophores, thereby resulting in amplified fluorescence signals. The two proposed methods exhibit good specificity and sensitivity, with detection limits of 0.327 nM and 0.049 nM Pb2+ for method 1 and method 2, respectively, and have been successfully applied to detect Pb2+ in river water and fish samples. Both detection methods employ the structure-switching aptamer probes and can be completed in two or three steps without the need for complex analytical instruments. Therefore, they have a broad prospect in the sensitive and simple detection of lead ion contamination in food and environmental samples.

A Radical-Generating Probe to Release Free Fluorophores and Identify Artemisinin-Sensitive Cancer Cells.

The smart light-up probes have been extensively developed to image various enzymes and other bioactive molecules. Upon activation, these probes result in light-up fluorophores that exist in a protein-bound or a free form. The difference between these two forms has not yet been reported. Here, we present a pair of smart light-up probes that generate a protein-bound fluorophore and a free fluorophore upon activation by heme. Probe 8 generated a radical-attached fluorophore that predominantly existed in the free form, while probe 10 generated an α,β-unsaturated ketone-attached fluorophore that showed extensive labeling of proteins. In live-cell imaging, probe 8 showed greater fluorescence intensity than probe 10 when low concentrations (0.1-5 μM) of the probes were used, but probe 8 was less fluorescent than probe 10 when the concentrations of the probes were high (10 μM). Finally, probe 8 was used to reflect the activation level of the endoperoxide bond in cancer cells and to effectively distinguish ART-sensitive cancer cells from ART-insensitive ones.

Single primer/self-template-powered isothermal amplification for single-molecule quantification of multiple DNA glycosylases

DNA glycosylase assumes a pivotal role in the preservation of genome integrity by recognizing and excising damaged bases. Herein, we develop a single primer/self-template-powered cascade rolling circle amplification (RCA) and apurinic/apyrimidinic endonuclease (APE1)-mediated signal amplification for simultaneous detection of human alkyladenine DNA glycosylase (hAAG) and uracil DNA glycosylase (UDG). The uniqueness of this approach lies in the use of custom-designed hairpin probes to establish a prerequisite for RCA: the conformational change of hairpin probe to circular template, which effectively suppress undesired non-specific amplification. We design two hairpin probes featuring elongated stem structure and 3′-phosphate (3′-PO4) modifications. The stems of hairpin probes are modified with glycosylase substrates and BER process can cleave hairpin probes, resulting in the generation of single-stranded DNAs (ssDNAs) with 3′-hydroxyl (3′-OH) ends. These ssDNAs can function as padlock probes to form circular template upon ligation by ligase. Ultimately, the self-template-initiated RCA and APE1-mediated signal amplification cascade occurs, generating a substantial number of free Cy3 and Cy5 fluorophores that can be simply visualized by single-molecule fluorescence detection. This method demonstrates excellent specificity and sensitivity, with a limit of detection (LOD) of 3.42 × 10-12 U/μL for hAAG and 2.41 × 10-12 U/μL for UDG. This method also can be used for screening of potential inhibitor and kinetic parameter measurement. Most importantly, this method enables accurate profiling of glycosylases expression levels in various cancer cell lines and detection of glycosylase activities at the single-cell level, offering a bright future in cancer detection, medical research, and precision medicine.

A Benzil- and BODIPY-Based Turn-On Fluorescent Probe for Detection of Hydrogen Peroxide.

Faced with rising threats of terrorism, environmental and health risks, achieving sensitive and selective detection of peroxide-based explosives (PEs) has become a global focus. In this study, a turn-on fluorescent probe (BOD) based on benzil (H2O2-recognition element) and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) derivative (fluorophore) was developed to sensitively and specifically detect hydrogen peroxide (H2O2). The synthesized BOD had a very weak fluorescence due to intramolecular donor-excited photo-induced electron transfer (d-PET) effect; however, it could emit a strong fluorescence since H2O2 selectively oxidized the benzil moiety and released free BODIPY fluorophore (BOD-COOH). As a result, the proposed BOD detected H2O2 in linear detection ranged from 25 to 125 µM with a detection limit of 4.41 µM. Meanwhile, the proposed BOD showed good selectivity toward H2O2, which is not affected by other common reactive oxygen species (ROS) and ions from explosive residues. In addition, a blue shift from 508 to 498 nm was observed in the absorption spectra upon addition of H2O2. More importantly, the BOD was successfully applied for rapid detection of H2O2 vapor with good sensitivity (down to 7 ppb), which holds great potential for practical use in public safety, forensic analysis and environmental monitoring.

Fluorescence Bar-Coding and Flowmetry Based on Dark State Transitions in Fluorescence Emitters.

Reversible dark state transitions in fluorophores represent a limiting factor in fluorescence-based ultrasensitive spectroscopy, are a necessary basis for fluorescence-based super-resolution imaging, but may also offer additional, largely orthogonal fluorescence-based readout parameters. In this work, we analyzed the blinking kinetics of Cyanine5 (Cy5) as a bar-coding feature distinguishing Cy5 from rhodamine fluorophores having largely overlapping emission spectra. First, fluorescence correlation spectroscopy (FCS) solution measurements on mixtures of free fluorophores and fluorophore-labeled small unilamellar vesicles (SUVs) showed that Cy5 could be readily distinguished from the rhodamines by its reversible, largely excitation-driven trans-cis isomerization. This was next confirmed by transient state (TRAST) spectroscopy measurements, determining the fluorophore dark state kinetics in a more robust manner, from how the time-averaged fluorescence intensity varies upon modulation of the applied excitation light. TRAST was then combined with wide-field imaging of live cells, whereby Cy5 and rhodamine fluorophores could be distinguished on a whole cell level as well as in spatially resolved, multiplexed images of the cells. Finally, we established a microfluidic TRAST concept and showed how different mixtures of free Cy5 and rhodamine fluorophores and corresponding fluorophore-labeled SUVs could be distinguished on-the-fly when passing through a microfluidic channel. In contrast to FCS, TRAST does not rely on single-molecule detection conditions or a high time resolution and is thus broadly applicable to different biological samples. Therefore, we expect that the bar-coding concept presented in this work can offer an additional useful strategy for fluorescence-based multiplexing that can be implemented on a broad range of both stationary and moving samples.

Near‐infrared fluorophores with absolute aggregation‐caused quenching and negligible fluorescence re‐illumination for in vivo bioimaging of nanocarriers

AbstractEnvironment‐responsive fluorophores with aggregation‐caused quenching (ACQ) properties have been applied to track nanocarriers with reduced artefacts caused by unbound or free fluorophores but suffer from incomplete fluorescence quenching and significant re‐illumination, which undermine bioimaging accuracy. Herein, through structural modifications to reinforce the hydrophobicity, planarity and rigidity of fluorophores with an aza‐BODIPY framework, probes featuring absolute ACQ (aACQ) and negligible re‐illumination are developed and evaluated in various nanocarriers. aACQ probes, FD‐B21 and FD‐C7, exhibit near‐infrared emission, high quantum yield, photostability, water sensitivity, and negligible re‐illumination in blood, plasma and 1% Tween‐80 in contrast to ACQ probe P2 and conventional probe DiR. All nanocarriers can be labeled efficiently by the tested fluorophores. Polymeric micelles (PMs) labeled by different aACQ probes manifest similar biodistribution patterns, which however differ from that of DiR‐labeled PMs and could be ascribed to the appreciable re‐illumination of DiR. Significantly lower re‐illumination is also found in aACQ probes (2%–3%) than DiR (20%–40%) in Caco‐2, Hela, and Raw264.7 cells. Molecular dynamics simulations unravel the molecular mechanisms behind aggregation and re‐illumination, supporting the hypothesis of planarity dependency. It is concluded that aACQ fluorophores demonstrate excellent water sensitivity and negligible fluorescence re‐illumination, making themselves useful tools for more accurate bioimaging of nanocarriers.

Revealing heterogeneity in correlation times of EGFP encapsulated in complex coacervate core micelles by analysis of fluorescence anisotropies

Encapsulation of enhanced green fluorescent protein (EGFP) in complex coacervate core micelles (C3Ms) can be established by mixing EGFP with diblock polymers at equal charge ratio. It has previously been shown that this encapsulation system is highly dynamic, implying existence of different populations; GFP free in solution or complexed with polymers (small complexes) and EGFP encapsulated in C3Ms. We performed time resolved fluorescence anisotropy experiments to determine the relative populations of EGFP encapsulated in C3Ms using three different fluorescence anisotropy decay analysis methods. First, Maximum Entropy Method (MEM) data analysis was employed for five different EGFP concentrations in C3Ms that were mixed with dark fluorescent proteins (10, 20, 30, 40 and 50% EGFP, respectively). In all cases, correlation-time distributions between 0.1 and 100 ns (on a logarithmic timescale) are clearly visible showing bimodal distribution. The distribution between 0.1 and 2.0 ns is due to homo-FRET between EGFP molecules packed in micelles and the distribution between 8 and 30 ns coincides with the correlation-time distribution of free EGFP in solution. The fraction of homo-FRET distribution linearly increases with increase of relative micellar EGFP concentrations. These MEM results were corroborated by two different analysis methods: global population analysis of all five fluorescence anisotropy decays arising from EGFP in micelles together with the one of free EGFP (direct analysis of anisotropies) and global associative population analysis of anisotropies by fitting parallel and perpendicular fluorescence decay components. In contrast to global analyses approaches, the MEM method directly reveals distributions of correlation times without any prior information about the sample. However, global associative analysis of anisotropies by fitting parallel and perpendicular fluorescence decay components is the only method that allows to estimate accurately fractions of free fluorophores in solution and encapsulated fluorophores.

A Computational-Experimental Approach to Unravel the Excited State Landscape in Heavy-Atom Free BODIPY-Related Dyes.

We performed a time-gated laser-spectroscopy study in a set of heavy-atom free single BODIPY fluorophores, supported by accurate, excited-state computational simulations of the key low-lying excited states in these chromophores. Despite the strong fluorescence of these emitters, we observed a significant fraction of time-delayed (microseconds scale) emission associated with processes that involved passage through the triplet manifold. The accuracy of the predictions of the energy arrangement and electronic nature of the low-lying singlet and triplet excited states meant that an unambiguous assignment of the main deactivation pathways, including thermally activated delayed fluorescence and/or room temperature phosphorescence, was possible. The observation of triplet state formation indicates a breakthrough in the “classic” interpretation of the photophysical properties of the renowned BODIPY and its derivatives.

Selective imaging of hydrogen peroxide over peroxynitrite by a boronate-based fluorescent probe engineered via a doubly activated electrophilicity-increasing strategy

Boronate-based fluorescent probes are widely used for the imaging of hydrogen peroxide (H2O2). However, their selectivity might be subjected to the interference of other reactive oxygen species, especially peroxynitrite (ONOO-), due to the reaction of boronates with ONOO- being several orders of magnitude faster than with H2O2. This work highlights a doubly activated electrophilicity-increasing strategy to develop a boronate-based fluorescent probe THMP for selective imaging of H2O2 over ONOO-, where a boronate-modified pyridiniumylacrylonitrile is grafted on the 2-(2′-hydroxy-3′-methoxyphenyl) benzothiazole scaffold. Specifically, the boronate oxidation of THMP by H2O2 leads to the release of the free fluorophore THMP-N, triggering a ratiometric fluorescence response from red to green. The presence of a doubly activated electrophilic site on the carbon-carbon double bond of THMP, by both the strong electron-withdrawing cyano group and the pyridinium moiety, allows selective oxidative cleavage of the double bond by ONOO- to an aldehyde HMBT-CHO, thereby excluding the interference of ONOO- in monitoring H2O2. With the aid of the probe, we successfully visualized increased levels of H2O2 during ferroptosis of HepG2 cells, and burst of H2O2 in brains of live mice during cerebral ischemia reperfusion injury.

A New Phenylazo-Based Fluorescent Probe for Sensitive Detection of Hypochlorous Acid in Aqueous Solution.

In this paper, we designed and synthesized a novel phenylazo-based fluorescent probe (RHN) for the sensing and imaging of hypochlorous acid (HClO) in mitochondria in living cells. In this process, HClO promoted the oxidation of the phenylazo group to generate a free Rhodol fluorophore moiety, which in turn restored strong fluorescence and realized the detection of HClO. As expected, RHN exhibited high selectivity, high sensitivity and rapid response, with detection limits as low as 22 nM (1.155 ng/mL). Importantly, the results of the cell imaging experiments indicated that RHN has the ability to image and sense HClO in mitochondria, which is of great significance for exploration of the specific role of HClO in both the immune system and diseases.

A Cell-Anchored and Self-Calibrated DNA Nanoplatform for in Situ Imaging and Quantification of Endogenous MicroRNA in Live Cells: Introducing Two Controls to Normalize the Sensing Signals

A Cell-Anchored and Self-Calibrated DNA Nanoplatform for in Situ Imaging and Quantification of Endogenous MicroRNA in Live Cells: Introducing Two Controls to Normalize the Sensing Signals

Single-Molecule, Non-Chromatic Discrimination in Binary Fluorophores Mixtures

SummarySingle biomolecule sensing often involves quantification of multiple fluorescent species, coupled for example to different DNAs or proteins resides. While chromatic separation of the fluorescent species is well-established and broadly used it involves several limitations, particularly when the total photon budget is limited. Here we theoretically and experimentally explore the use of time-resolved fluorescence via Time Correlated Single Photon Counting (TCSPC) to accurately quantify multiple fluorescent species. A modified maximum likelihood estimator (MLE) is introduced to include two fluorophore species, with the compensation of the instrument response. We apply this algorithm to simulated data of a simplified two fluorescent species model, as well as to experimental data of free fluorophores mixtures and doubly labelled proteins in order to estimate the errors in the two species ratios as a function of photon budget available. Moreover, focusing on the case of labeled proteins in which the ratios of the two species per molecule is a discrete variable subject to the chemical labeling numbers of the two dyes, we obtain that between 1,000 to 2,000 photons can already provide an accurate estimation of the dyes’ ratio in labelled Ovalbumin proteins. These values correspond to roughly 100 to 200 photons per fluorophore suggesting a realistic path for dyes ratio determination from a single passage of a protein in the detection volume in roughly 10 ms timescale. Our results highlight the way in which temporal limitations of the TCSPC technique could hinder its implementation in systems with fast occurring events such as translocation of biomolecules through nanopores, or fast diffusion in single-molecule burst analyses experiments and provide estimation for the desired photon integration time.

Rapid Characterization and Quantification of Extracellular Vesicles by Fluorescence-Based Microfluidic Diffusion Sizing.

Extracellular vesicles (EVs) are emerging as promising diagnostic and therapeutic tools for a variety of diseases. The characterization of EVs requires a series of orthogonal techniques that are overall time- and material-consuming. Here, a microfluidic device is presented that exploits the combination of diffusion sizing and multiwavelength fluorescence detection to simultaneously provide information on EV size, concentration, and composition. The latter is achieved with the nonspecific staining of lipids and proteins combined with the specific staining of EV markers such as EV-associated tetraspanins via antibodies. The device can be operated as a single-step immunoassay thanks to the integrated separation and quantification of free and EV-bound fluorophores. This microfluidic technique is capable of detecting and quantifying components associated to EV subtypes and impurities and thus to measure EV purity in a time scale of minutes, requiring less than 5 µL of sample and minimal sample handling before the analysis. Moreover, the analysis is performed directly in solution without immobilization steps. Therefore, this method can accelerate screening of EV samples and aid the evaluation of sample reproducibility, representing an important complementary tool to the current array of biophysical methods for EV characterization, particularly valuable for instance for bioprocess development.

Interventional NIR Fluorescence Imaging of Cancer: Review on Next Generation of Dye-Loaded Protein-Based Nanoparticles for Real-Time Feedback During Cancer Surgery

The use of fluorescence imaging technique for visualization, resection and treatment of cancerous tissue, attained plenty of interest once the promise of whole body and deep tissue near-infrared (NIR) imaging emerged. Why is NIR so desired? Contrast agents with optical properties in the NIR spectral range offer an upgrade for the diagnosis and treatment of cancer, by dint of the deep tissue penetration of light in the NIR region of the electromagnetic spectrum, also known as the optical window in biological tissue. Thus, the development of a new generation of NIR emitting and absorbing contrast agents able to overcome the shortcomings of the basic free dye administration is absolutely essential. Several examples of nanoparticles (NPs) have been successfully implemented as carriers for NIR dye molecules to the tumour site owing to their prolonged blood circulation time and enhanced accumulation within the tumour, as well as their increased fluorescence signal relative to free fluorophore emission and active targeting of cancerous cells. Due to their versatile structure, good biocompatibility and capability to efficiently load dyes and bioconjugate with diverse cancer-targeting ligands, the research area of developing protein-based NPs encapsulated or conjugated with NIR dyes is highly promising but still in its infancy. The current review aims to provide an up-to-date overview on the biocompatibility, specific targeting and versatility offered by protein-based NPs loaded with different classes of NIR dyes as next-generation fluorescent agents. Moreover, this study brings to light the newest and most relevant advances involving the state-of-the-art NIR fluorescent agents for the real-time interventional NIR fluorescence imaging of cancer in clinical trials.

Palladium zero-mode waveguides for optical single-molecule detection with nanopores

Holes in metal films do not allow the propagation of light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called zero-mode waveguides (ZMWs). Molecules, on the other hand, can still pass through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW and thereby traverse from the dark region to the illuminated side, upon which they emit fluorescent light. This is beneficial both for background suppression and to prevent premature bleaching. We use palladium as a novel metal-film material for ZMWs, which is advantageous compared to conventionally used metals. We demonstrate that it is possible to simultaneously detect translocations of individual free fluorophores of different colours. Labelled DNA and protein biomolecules can also be detected at the single-molecule level with a high signal-to-noise ratio and at high bandwidth, which opens the door to a variety of single-molecule biophysics studies.

DNA-Based Nanocarriers to Enhance the Optoacoustic Contrast of Tumors In Vivo.

Optoacoustic tomography (OT) enables non-invasive deep tissue imaging of optical contrast at high spatio-temporal resolution. The applications of OT in cancer imaging often rely on the use of molecular imaging contrast agents based on near-infrared (NIR) dyes to enhance contrast at the tumor site. While these agents afford excellent biocompatibility and minimal toxicity, they present limited optoacoustic signal generation capability and rapid renal clearance, which can impede their tumor imaging efficacy. In this work, a synthetic strategy to overcome these limitations utilizing biodegradable DNA-based nanocarrier (DNA-NC) platforms is introduced. DNA-NCs enable the incorporation of NIR dyes (in this case, IRDye 800CW) at precise positions to enable fluorescence quenching and maximize optoacoustic signal generation. Furthermore, these DNA-NCs show a prolonged blood circulation compared to the native fluorophores, facilitating tumor accumulation by the enhanced permeability and retention (EPR) effect. In vivo imaging of tumor xenografts in mice following intravenous administration of DNA-NCs reveals enhanced OT signals at 24 h when compared to free fluorophores, indicating promise for this method to enhance the optoacoustic signal generation capability and tumor uptake of clinically relevant NIR dyes.