Stable, Bright, and Long-Fluorescence-Lifetime Dyes for Deep-Near-Infrared Bioimaging

Extending the emission peak tail of indole cyanine for deep-near-infrared bioimaging

We propose a novel strategy for tailoring the structure of fluorescent molecules to achieve emission at the tail end of the NIR-II window. The favorable spectroscopic properties and low cytotoxicity of YNs make them powerful tools for bioimaging. Notably, YN-4 exhibits a brightness 2.5 times greater than YN-3, 6 times that of IR-783, and 5 times that of ICG. This enhanced brightness enabled high-resolution imaging of mouse thoracic and abdominal cavities, tumor vasculature, and real-time monitoring of gastrointestinal motility using YN-4. Furthermore, covalent grafting of glucose onto the YN-Glu scaffold significantly improved tumor-targeting capability and facilitated tracking of glucose metabolism. This work aims to extend the application of fluorescent molecule imaging beyond the NIR-IIa window.

High Fluorescence of Phytochromes Does Not Require Chromophore Protonation

Fluorescing proteins emitting in the near-infrared region are of high importance in various fields of biomedicine and applied life sciences. Promising candidates are phytochromes that can be engineered to a small size and genetically attached to a target system for in vivo monitoring. Here, we have investigated two of these minimal single-domain phytochromes, miRFP670nano3 and miRFP718nano, aiming at a better understanding of the structural parameters that control the fluorescence properties of the covalently bound biliverdin (BV) chromophore. On the basis of resonance Raman and time-resolved fluorescence spectroscopy, it is shown that in both proteins, BV is deprotonated at one of the inner pyrrole rings (B or C). This protonation pattern, which is unusual for tetrapyrroles in proteins, implies an equilibrium between a B- and C-protonated tautomer. The dynamics of the equilibrium are slow compared to the fluorescence lifetime in miRFP670nano3 but much faster in miRFP718nano, both in the ground and excited states. The different rates of proton exchange are most likely due to the different structural dynamics of the more rigid and more flexible chromophore in miRFP670nano3 and miRFP718nano, respectively. We suggest that these structural properties account for the quite different fluorescent quantum yields of both proteins.

Dihydropyridopyrazine Functionalized Xanthene: Generating Stable NIR Dyes with Small-Molecular Weight by Enhanced Charge Separation

Near-infrared region (NIR; 650-1700 nm) dyes offer many advantages over traditional dyes with absorption and emission in the visible region. However, developing new NIR dyes, especially organic dyes with long wavelengths, small molecular weight, and excellent stability and biocompatibility, is still quite challenging. Herein, we present a general method to enhance the absorption and emission wavelengths of traditional fluorophores by simply appending a charge separation structure, dihydropyridopyrazine. These novel NIR dyes not only exhibited greatly redshifted wavelengths compared to their parent dyes, but also displayed a small molecular weight increase together with retained stability and biocompatibility. Specifically, dye NIR-OX, a dihydropyridopyra-zine derivative of oxazine with a molecular mass of 386.2 Da, exhibited an absorption at 822 nm and an emission extending to 1200 nm, making it one of the smallest molecular-weight NIR-II emitting dyes. Thanks to its rapid metabolism and long wave-length, NIR-OX enabled high-contrast bioimaging and assessment of cholestatic liver injury in vivo and also facilitated the evalua-tion of the efficacy of liver protection medicines against cholestatic liver injury.

Steric protection of near-infrared fluorescent dyes for enhanced bioimaging

Near-fluorescent (NIR) dyes that absorb and emit light in the wavelength range of 650-1700 nm are well-suited for bioimaging due to the improved image contrast and increased penetration of the long-wavelength light through biological tissue. However, the imaging performance of NIR fluorescent dyes is limited by several inherent photophysical and physicochemical properties including, low fluorescence quantum yield, high chemical and photochemical reactivity, propensity to self-aggregate in water, non-specific association with off-target biological sites, and non-optimal pharmacokinetic profiles in living subjects. In principle, all these drawbacks can be alleviated by steric protection which is a structural process that surrounds the fluorophore with bulky groups that block undesired intermolecular interactions. The literature methods to sterically protect a long-wavelength dye can be separated into two general strategies, non-covalent dye encapsulation and covalent steric appendage. Illustrative examples of each method show how steric protection improves bioimaging performance by providing: (a) increased fluorescence brightness, (b) higher fluorophore ground state stability, (c) decreased photobleaching, and (d) superior pharmacokinetic profile. Some sterically protected dyes are commercially available and further success with future systems will require experts in chemistry, microscopy, cell biology, medical imaging, and clinical medicine to work closely as interdisciplinary teams.

Ultrabright Dibenzofluoran-Based Polymer Dots with NIR-IIa Emission Maxima and Unusual Large Stokes Shifts for 3D Rotational Stereo Imaging

Emerging organic molecules with emissions in the second near-infrared (NIR-II) region are garnering significant attention. Unfortunately, achieving accountable organic emission intensity over the NIR-IIa (1300 nm) region faces challenges due to the intrinsic energy gap law. Up to the current stage, all reported organic NIR-IIa emitters belong to polymethine-based dyes with small Stokes shifts (<50 nm) and low quantum yield (QY; ≤0.015%). However, such polymethines have proved to cause self-absorption with constrained emission brightness, limiting advanced development in deep-tissue imaging. Here a new NIR-IIa scaffold based on rigid and highly conjugated dibenzofluoran core terminated by amino-containing moieties that reveal emission peaks of 1230-1305 nm is designed. The QY is at least 10 times higher than all synthesized or reported NIR-IIa polymethines with extraordinarily large Stokes shifts of 370-446 nm. DBF-BJ is further prepared as a polymer dot to demonstrate its in vivo 3D stereo imaging of mouse vasculature with a 1400 nm long-pass filter.

A planar electronic acceptor motif contributing to NIR-II AIEgen with combined imaging and therapeutic applications

Designing molecules with donor-acceptor-donor (D-A-D) architecture plays an important role in obtaining second near-infrared region (NIR-II, 1000-1700 nm) fluorescent dyes for biomedical applications; however, this always comes with a challenge due to very limited electronic acceptors. On the other hand, to endow NIR-II fluorescent dyes with combined therapeutic applications, trivial molecular design is indispensable. Herein, we propose a pyrazine-based planar electronic acceptor with a strong electron affinity, which can be used to develop NIR-II fluorescent dyes. By structurally attaching two classical triphenylamine electronic donors to it, a basic D-A-D module, namely Py-NIR, can be generated. The planarity of the electronic acceptor is crucial to induce a distinct NIR-II emission peaking at ∼1100 nm. The unique construction of the electronic acceptor can cause a twisted and flexible molecular conformation by the repulsive effect between the donors, which is essential to the aggregation-induced emission (AIE) property. The tuned intramolecular motions and twisted D-A pair brought by the electronic acceptor can lead to a remarkable photothermal conversion with an efficiency of 56.1% and induce a type I photosensitization with a favorable hydroxyl radical (OH˙) formation. Note that no additional measures are adopted in the molecular design, providing an ideal platform to realize NIR-II fluorescent probes with synergetic functions based on such an acceptor. Besides, the nanoparticles of Py-NIR can exhibit excellent NIR-II fluorescence imaging towards orthotopic 4T1 breast tumors in living mice with a high sensitivity and contrast. Combined with photothermal imaging and photoacoustic imaging caused by the thermal effect, the imaging-guided photoablation of tumors can be well performed. Our work has created a new opportunity to develop NIR-II fluorescent probes for accelerating biomedical applications.

A Nanographene-Porphyrin Hybrid for Near-Infrared-Ii Phototheranostics

Photoacoustic imaging (PAI)-guided photothermal therapy (PTT) in the second near-infrared (NIR-II, 1000-1700 nm) window has been attracting attention as a promising cancer theranostic platform. Here, it is reported that the π-extended porphyrins fused with one or two nanographene units (NGP-1 and NGP-2) can serve as a new class of NIR-responsive organic agents, displaying absorption extending to ≈1000 and ≈1400 nm in the NIR-I and NIR-II windows, respectively. NGP-1 and NGP-2 are dispersed in water through encapsulation into self-assembled nanoparticles (NPs), achieving high photothermal conversion efficiency of 60% and 69%, respectively, under 808 and 1064 nm laser irradiation. Moreover, the NIR-II-active NGP-2-NPs demonstrated promising photoacoustic responses, along with high photostability and biocompatibility, enabling PAI and efficient NIR-II PTT of cancer in vivo.

Surfactant-based supramolecular dye assembly: A highly selective and economically viable platform for quantification of heparin antidote

Herein, we have employed a supramolecular assembly of a cationic dye, LDS-698 and a common surfactant sodium dodecyl sulfate (SDS) as a turn-on fluorescent sensor for protamine (Pr) detection. Addition of cationic Pr to the solution of dye-surfactant complex brings negatively charged SDS molecules together through strong electrostatic interaction, assisting aggregation of SDS way before its critical micellar concentration (CMC). These aggregates encapsulate the dye molecules within their hydrophobic region, arresting non-radiative decay channels of the excited dye. Thus, the LDS-698•SDS assembly displays substantial enhancement in fluorescence intensity that follows a nice linear trend with Pr concentration, providing limit of detection (LOD) for Pr as low as 3.84(±0.11) nM in buffer, 124.4(±6.7) nM in 1% human serum and 28.3(±0.5) nM in 100% human urine. Furthermore, high selectivity, low background signal, large stokes shift, and emission in the biologically favorable deep-red region make the studied assembly a promising platform for Pr sensing. As of our knowledge it is the first ever Pr sensory platform, using a very common surfactant (SDS), which is economically affordable and very easily available in the market. This innovative approach can replace the expensive, exotic and specialized chemicals considered for the purpose and thus showcase its potential in practical applications.

2X-Rhodamine: A Bright and Fluorogenic Scaffold for Developing Near-Infrared Chemigenetic Indicators

Chemigenetic fusion of synthetic dyes with genetically encoded protein tags presents a promising avenue for in vivo imaging. However, its full potential has been hindered by the lack of bright and fluorogenic dyes operating in the "tissue transparency" near-infrared window (NIR, 700-1700 nm). Here, we report 2X-rhodamine (2XR), a novel bright scaffold that allows for the development of live-cell-compatible, NIR-excited variants with strong fluorogenicity beyond 1000 nm. 2XR utilizes a rigidified π-skeleton featuring dual atomic bridges and functions via a spiro-based fluorogenic mechanism. This design affords longer wavelengths, higher quantum yield (ΦF = 0.11), and enhanced fluorogenicity in water when compared to the phosphine oxide-cored, or sulfone-cored rhodamine, the NIR fluorogenic benchmarks currently used. We showcase their bright performance in video-rate dynamic imaging and targeted deep-tissue molecular imaging in vivo. Notably, we develop a 2XR variant, 2XR715-HTL, an NIR fluorogenic ligand for the HaloTag protein, enabling NIR genetically encoded calcium sensing and the first demonstration of in vivo chemigenetic labeling beyond 1000 nm. Our work expands the library of NIR fluorogenic tools, paving the way for in vivo imaging and sensing with the chemigenetic approach.

Boosting Luminescence Efficiency of Near-Infrared-II Aggregation-Induced Emission Luminogens via a Mash-Up Strategy of π-Extension and Deuteration for Dual-Model Image-Guided Surgery

The simultaneous pursuit of accelerative radiative and restricted nonradiative decay is of tremendous significance to construct high-luminescence-efficiency fluorophores in the second near-infrared wavelength window (NIR-II), which is seriously hindered by the energy gap laws. Herein, a mash-up strategy of π-extension and deuteration is proposed to efficaciously ameliorate the knotty problem. By extending the π-conjugation of the aromatic fragment and introducing an isotope effect to the aggregation-induced emission luminogen (AIEgen), an improved oscillator strength (f), coupled with suppressed deformation and high-frequency oscillation in the excited state, are successively implemented. In this case, a faster rate of radiative decay (kr) and restricted nonradiative decay (knr) are simultaneously achieved. Moreover, the preeminent emissive property of AIEgen in the molecular state could be commendably inherited by the aggregates. The corresponding NIR-II emissive AIEgen-based nanoparticles display high brightness, large Stokes shift, and superior photostability simultaneously, which can be applied for image-guided cancer and sentinel lymph node (SLN) surgery. This work thus provides a rational roadmap to improve the luminescence efficiency of NIR-II fluorophores for biomedical applications.

Ultra-photostable small-molecule dyes facilitate near-infrared biophotonics

Long-wavelength, near-infrared small-molecule dyes are attractive in biophotonics. Conventionally, they rely on expanded aromatic structures for redshift, which comes at the cost of application performance such as photostability, cell permeability, and functionality. Here, we report a ground-state antiaromatic strategy and showcase the concise synthesis of 14 cationic aminofluorene dyes with mini structures (molecular weights: 299-504 Da) and distinct spectra covering 700-1600 nm. Aminofluorene dyes are cell-permeable and achieve rapid renal clearance via a simple 44 Da carboxylation. This accelerates optical diagnostics of renal injury by 50 min compared to existing macromolecular approaches. We develop a compact molecular sensing platform for in vivo intracellular sensing, and demonstrate the versatile applications of these dyes in multispectral fluorescence and optoacoustic imaging. We find that aromaticity reversal upon electronic excitation, as indicated by magnetic descriptors, not only reduces the energy bandgap but also induces strong vibronic coupling, resulting in ultrafast excited-state dynamics and unparalleled photostability. These results support the argument for ground-state antiaromaticity as a useful design rule of dye development, enabling performances essential for modern biophotonics.

Investigating Oxidative Stress Associated with Myocardial Fibrosis by High-Fidelity Visualization and Accurate Evaluation of Mitochondrial GSH Levels

Myocardial fibrosis is frequently accompanied by elevated levels of oxidative stress. Mitochondrial glutathione (mGSH), an essential biomolecule for maintaining redox homeostasis in mitochondria, could serve as an effective indicator for investigating the oxidative stress associated with myocardial fibrosis. In this study, a ratiometric fluorescent probe named Mito-NS6, capable of being anchored in mitochondria and reversibly responding to GSH with an appropriate dissociation equilibrium constant, was rationally designed and utilized to visualize and evaluate the changes of mGSH levels caused by oxidative stress in myocardial fibrosis. Benefiting from the good performance of Mito-NS6, we successfully achieved the quantification of mGSH in cardiac fibroblasts using a confocal laser-scanning microscope, revealing that salvianolic acid B (SalB) can act as an effective drug to alleviate myocardial fibrosis through depressing oxidative stress. Moreover, we employed ratio fluorescence imaging to track the fluctuation in GSH levels within a mice model of myocardial fibrosis induced by isoproterenol and found that myocardial fibrosis caused a higher oxidative stress level in myocardial tissue as well as heart organs. These results provide a novel point of view for the diagnosis and treatment of myocardial fibrosis.

Tuning Shortwave-Infrared J-aggregates of Aromatic Ring-Fused Aza-BODIPYs by Peripheral Substituents for Combined Photothermal and Photodynamic Therapies at Ultralow Laser Power

Achieving photothermal therapy (PTT) at ultralow laser power density is crucial for minimizing photo-damage and allowing for higher maximum permissible skin exposure. However, this requires photothermal agents to possess not just superior photothermal conversion efficiency (PCE), but also exceptional near-infrared (NIR) absorptivity. J-aggregates, exhibit a significant redshift and narrower absorption peak with a higher extinction coefficient. Nevertheless, achieving predictable J-aggregates through molecular design remains a challenge. In this study, we successfully induced desirable J-aggregation (λabs max : 968 nm, ϵ: 2.96×105  M-1  cm-1 , λem max : 972 nm, ΦFL : 6.2 %) by tuning electrostatic interactions between π-conjugated molecular planes through manipulating molecular surface electrostatic potential of aromatic ring-fused aza-BODIPY dyes. Notably, by controlling the preparation method for encapsulating dyes into F-127 polymer, we were able to selectively generate H-/J-aggregates, respectively. Furthermore, the J-aggregates exhibited two controllable morphologies: nanospheres and nanowires. Importantly, the shortwave-infrared J-aggregated nanoparticles with impressive PCE of 72.9 % effectively destroyed cancer cells and mice-tumors at an ultralow power density of 0.27 W cm-2 (915 nm). This phototherapeutic nano-platform, which generates predictable J-aggregation behavior, and can controllably form J-/H-aggregates and selectable J-aggregate morphology, is a valuable paradigm for developing photothermal agents for tumor-treatment at ultralow laser power density.

Chemical Approaches to Optimize the Properties of Organic Fluorophores for Imaging and Sensing

Organic fluorophores are indispensable tools in cells, tissue and in vivo imaging, and have enabled much progress in the wide range of biological and biomedical fields. However, many available dyes suffer from insufficient performances, such as short absorption and emission wavelength, low brightness, poor stability, small Stokes shift, and unsuitable permeability, restricting their application in advanced imaging technology and complex imaging. Over the past two decades, many efforts have been made to improve these performances of fluorophores. Starting with the luminescence principle of fluorophores, this review clarifies the mechanisms of the insufficient performance for traditional fluorophores to a certain extent, systematically summarizes the modified approaches of optimizing properties, highlights the typical applications of the improved fluorophores in imaging and sensing, and indicates existing problems and challenges in this area. This progress not only proves the significance of improving fluorophores properties, but also provide a theoretical guidance for the development of high-performance fluorophores.

Synthesis and Properties of Bright Red-to-NIR BODIPY Dyes for Targeting Fluorescence Imaging and Near-Infrared Photothermal Conversion

An efficient synthesis of 3-pyrrolylBODIPY dyes has been developed from a rational mixture of various aromatic aldehydes and pyrrole in a straightforward condensation reaction, followed by in situ successively oxidative nucleophilic substitution using a one-pot strategy. These resultant 3-pyrrolylBODIPYs without blocking substituents not only exhibit the finely tunable photophysical properties induced by the flexible meso-aryl substituents but also serve as a valuable synthetic framework for further selective functionalization. As a proof of such potential, one 3-pyrrolylBODIPY dye (581/603 nm) through the installation of the morpholine group is applicable for lysosome-targeting imaging. Furthermore, an ethene-bridged 3,3'-dipyrrolylBODIPY dimer was constructed, which displayed a near-infrared (NIR) emission extended to 1200 nm with a large fluorescence brightness (2840 M-1 cm-1). The corresponding dimer nanoparticles (NPs) afforded a high photothermal conversion efficiency (PCE) value of 72.5%, eventually resulting in favorable photocytotoxicity (IC50 = 9.4 μM) and efficient in vitro eradication of HeLa cells under 808 nm laser irradiation, highlighting their potential application for photothermal therapy in the NIR window.

Multiplexed near infrared fluorescence lifetime imaging in turbid media

Significance

Fluorescence lifetime imaging (FLI) plays a pivotal role in enhancing our understanding of biological systems, providing a valuable tool for non-invasive exploration of biomolecular and cellular dynamics, both in vitro and in vivo. Its ability to selectively target and multiplex various entities, alongside heightened sensitivity and specificity, offers rapid and cost-effective insights.

Aim

Our aim is to investigate the multiplexing capabilities of near-infrared (NIR) FLI within a scattering medium that mimics biological tissues. We strive to develop a comprehensive understanding of FLI's potential for multiplexing diverse targets within a complex, tissue-like environment.

Approach

We introduce an innovative Monte Carlo (MC) simulation approach that accurately describes the scattering behavior of fluorescent photons within turbid media. Applying phasor analyses, we enable the multiplexing of distinct targets within a single FLI image. Leveraging the state-of-the-art single-photon avalanche diode (SPAD) time-gated camera, SPAD512S, we conduct experimental wide-field FLI in the NIR regime.

Results

Our study demonstrates the successful multiplexing of dual targets within a single FLI image, reaching a depth of 1 cm within tissue-like phantoms. Through our novel MC simulation approach and phasor analyses, we showcase the effectiveness of our methodology in overcoming the challenges posed by scattering media.

Conclusions

This research underscores the potential of NIR FLI for multiplexing applications in complex biological environments. By combining advanced simulation techniques with cutting-edge experimental tools, we introduce significant results in the non-invasive exploration of biomolecular dynamics, to advance the field of FLI research.

Au nanodyes as enhanced contrast agents in wide field near infrared fluorescence lifetime imaging

The near-infrared (NIR) range of the electromagnetic (EM) spectrum offers a nearly transparent window for imaging tissue. Despite the significant potential of NIR fluorescence-based imaging, its establishment in basic research and clinical applications remains limited due to the scarcity of fluorescent molecules with absorption and emission properties in the NIR region, especially those suitable for biological applications. In this study, we present a novel approach by combining the widely used IRdye 800NHS fluorophore with gold nanospheres (GNSs) and gold nanorods (GNRs) to create Au nanodyes, with improved quantum yield (QY) and distinct lifetimes. These nanodyes exhibit varying photophysical properties due to the differences in the separation distance between the dye and the gold nanoparticles (GNP). Leveraging a rapid and highly sensitive wide-field fluorescence lifetime imaging (FLI) macroscopic set up, along with phasor based analysis, we introduce multiplexing capabilities for the Au nanodyes. Our approach showcases the ability to differentiate between NIR dyes with very similar, short lifetimes within a single image, using the combination of Au nanodyes and wide-field FLI. Furthermore, we demonstrate the uptake of Au nanodyes by mineral-oil induced plasmacytomas (MOPC315.bm) cells, indicating their potential for in vitro and in vivo applications.

Molecular Engineering of Sulfone-Xanthone Chromophore for Enhanced Fluorescence Navigation

Enriching the palette of high-performance fluorescent dyes is vital to support the frontier of biomedical imaging. Although various rhodamine skeletons remain the premier type of small-molecule fluorophores due to the apparent high brightness and flexible modifiability, they still suffer from the inherent defect of small Stokes shift due to the nonideal fluorescence imaging signal-to-background ratio. Especially, the rising class of fluorescent dyes, sulfone-substituted xanthone, exhibits great potential, but low chemical stability is also pointed out as the problem. Molecular engineering of sulfone-xanthone to obtain a large Stokes shift and high stability is highly desired, but it is still scarce. Herein, we present the combination modification method for optimizing the performance of sulfone-xanthone. These redesigned fluorescent skeletons owned greatly improved stability and Stokes shift compared with the parent sulfone-rhodamine. To the proof of bioimaging capacity, annexin protein-targeted peptide LS301 was introduced to the most promising dyes, J-S-ARh, to form the tumor-targeted fluorescent probe, J-S-LS301. The resulting probe, J-S-LS301, can be an outstanding fluorescence tool for the orthotopic transplantation tumor model of hepatocellular carcinoma imaging and on-site pathological analysis. In summary, the combination method could serve as a basis for rational optimization of sulfone-xanthone. Overall, the chemistry reported here broadens the scope of accessible sulfone-xanthone functionality and, in turn, enables to facilitate the translation of biomedical research toward the clinical domain.

High-Performance Near-Infrared Chlorinated Rylenecarboximide Fluorophores via Consecutive C-N and C-C Bond Formation

A new class of near-infrared (NIR) fluorophores, PAI, is obtained by consecutive C-N/C-C bond formation between diphenylamines and 9,10-dibromoperylenecarboximide. Owing to the rigid structure, extended π-conjugation and pronounced push-pull substitution, these fluorophores show emission maxima up to 804 nm and large Stokes shifts. The extraordinarily high fluorescence quantum yields from 47 % to 70 % are attributed to chloro substitution in the bay positions of the perylene core. These characteristics, together with high photostability, qualify them as useful NIR emitters for applications as biomarkers and security inks.

Synthesis of a new fluorophore: wavelength-tunable bisbenzo[f]isoindolylidenes

The creation of new functional molecules is a central task in chemical synthesis. Herein, we report the synthesis of a new type of fluorophore, bisbenzo[f]isoindolylidenes, from easily accessible dipropargyl benzenesulfonamides. Wavelength-tunable fluorophores emitting strong fluorescence of green to red light were obtained in this reaction. Late-stage modifications and incorporation of bioactive molecules into these fluorophores give rise to potential applications in biological studies. Detailed computational and experimental studies were conducted to elucidate the mechanism, and suggest a reaction sequence involving Garratt-Braverman type cyclization, isomerization, fragmentation, dimerization and oxidation.

Electron-Withdrawing Substituents Allow Boosted NIR-II Fluorescence in J-Type Aggregates for Bioimaging and Information Encryption

Developing molecular fluorophores with enhanced fluorescence in aggregate state for the second near-infrared (NIR-II) imaging is highly desirable but remains a tremendous challenge due to the lack of reliable design guidelines. Herein, we report an aromatic substituent strategy to construct highly bright NIR-II J-aggregates. Introduction of electron-withdrawing substituents at 3,5-aryl and meso positions of classic boron dipyrromethene (BODIPY) skeleton can promote slip-stacked J-type arrangement and further boost NIR-II fluorescence of J-aggregates via increased electrostatic repulsion and intermolecular hydrogen bond interaction. Notably, NOBDP-NO2 with three nitro groups (-NO2 ) shows intense NIR-II fluorescence at 1065 nm and high absolute quantum yield of 3.21 % in solid state, which can be successfully applied in bioimaging, high-level encoding encryption, and information storage. Moreover, guided by this electron-withdrawing substituent strategy, other skeletons (thieno-fused BODIPY, aza-BODIPY, and heptamethine cyanine) modified with -NO2 are converted into J-type aggregates with enhanced NIR-II fluorescence, showing great potential to convert aggregation caused emission quenching (ACQ) dyes into brilliant J-aggregates. This study provides a universal method for construction of strong NIR-II emissive J-aggregates by rationally manipulating molecular packing and establishing relationships among molecular structures, intermolecular interactions, and fluorescence properties.

A deep-red fluorophore based on naphthothiadiazole as emitter with hybridized local and charge transfer and ambipolar transporting properties for electroluminescent devices

Herein, we report the synthesis and characterization of an efficient ambipolar charge-carrier-transporting deep-red fluorophore (TPECNz) based on a donor-acceptor-donor (D-A-D)-type molecule and its application as a non-doped emitter in an organic light-emitting diode (OLED). The fluorophore TPECNz contains naphtho[2,3-c][1,2,5]thiadiazole (Nz) as a strong acceptor unit symmetrically functionalized with N-(4-(1,2,2-triphenylvinyl)phenyl)carbazole as a donor and aggregation-induced emission (AIE) luminogen. The experimental (solvatochromic and emission in THF/water mixtures studies) and theoretical investigations prove that TPECNz retains cooperative hybridized local and charge transfer (HLCT) and weak AIE features. Thanks to its D-A-D-type structure with a proper twist angle between the D and A units, a strong electron deficiency of the Nz unit, and electron-donating and hole-transporting natures of carbazole, TPECNz exhibits a strong deep red emission (λem = 648 nm) with a high fluorescence quantum yield of 96%, outstanding thermal property (Tg = 236 °C), and ambipolar charge-carrier-transporting property with a decent balance of mobility of electrons (1.50 × 10-5 cm2 V-1 s-1) and holes (4.42 × 10-6 cm2 V-1 s-1). TPECNz is successfully employed as a non-doped emitter in an OLED which displays deep red electroluminescent emission peaked at 659 nm with CIE coordinates of (0.664, 0.335)), an EQEmax of 3.32% and exciton utilization efficiency (EUE) of 47%.

Nucleophile-Triggered π-Topological Transformation: A New Synthetic Approach to Near-Infrared-Emissive Rhodamines

We describe a π-topological transformation-based synthetic method for the preparation of a new type of near-infrared (NIR)-emissive rhodamine dye called Polymethine-embedded Rhodamine Fluorophore (PeR Fluor). In contrast to conventional NIR-emissive dyes that require tedious synthetic steps and/or a high cost, linear fully π-conjugated PeR Fluor can be regioselectively prepared in one step by mixing different nucleophiles with ABPXs, a family of rhodamines with a cross-conjugated structure. PeR Fluor exhibits bright NIR fluorescence emission and high photostability owing to the cooperative π-electron system of rhodamines and polymethine scaffolds. Large bathochromic shifts of the absorption and fluorescence emission maxima can be achieved by modifying the N-substituted group to obtain NIR-absorbing/emitting PeR Fluor. We also demonstrate the stimulus-responsive functionality of PeR Fluor through the addition of chemicals (acid/base), which shows switchable NIR and visible fluorescence response. Our π-topological transformation-based synthetic method is a promising approach to produce new functionalized rhodamine dyes.

Imaging of Carbonic Anhydrase Level in Epilepsy with an Environment-Sensitive Fluorescent Probe

Carbonic anhydrases (CAs) participate in various physiological and pathological activities by catalyzing the interconversion between carbon dioxide and bicarbonate ions. Under normal circumstances, they guarantee that the relevant biological reactions in our body occur within an appropriate time scale. Abnormal expression or activity alteration of CAs is closely related to the pathogenesis of diverse diseases. This work reports an inhibitor-directed fluorescent probe FMRs-CA for the detection of CAs. Excellent selectivity, favorable biocompatibility, and desirable blood-brain barrier (BBB) penetration endow the probe with the ability to image the fluctuation of CAs in cells and mice. We achieved in situ visualization of the increased CAs in hypoxic cells with this probe. Additionally, probe FMRs-CA was mainly enriched within the liver and gradually metabolized by the liver. With the help of FMRs-CA, the increase of CAs in epileptic mouse brains was revealed first from the perspective of imaging, providing the mechanism connection between abnormal CA expressions and epilepsy.

Molecular fluorescent sensors for in vivo imaging

Small-molecule fluorophores are powerful tools for biological research. They have enabled researchers to study cellular architecture and decipher biological processes. Responsive fluorescent sensors have enabled the study of a wide range of analytes and their effects on biological phenomena in situ. The application of fluorescent sensors to studies in living organisms is complicated by challenges such as biocompatibility, chemostability, photostability and sufficient penetration of light through living tissues. Translation to in vivo imaging is therefore not straightforward and requires innovative approaches. Recent advances in the design of fluorophores with improved photophysical properties and the development of long-wavelength-emitting fluorophore scaffolds that can be modularly functionalised with targeting and sensing groups have allowed the application of fluorogenic, ratiometric and reversible sensors in vivo.

Spontaneously Blinking Rhodamine Dyes for Single-Molecule Localization Microscopy

Single-molecule localization microscopy (SMLM) has found extensive applications in various fields of biology and chemistry. As a vital component of SMLM, fluorophores play an essential role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores has greatly simplified the experimental setups and extended the imaging duration of SMLM. To support this crucial development, this review provides a comprehensive overview of the development of spontaneously blinking rhodamines from 2014 to 2023, as well as the key mechanistic aspects of intramolecular spirocyclization reactions. We hope that by offering insightful design guidelines, this review will contribute to accelerating the advancement of super-resolution imaging technologies.

Strategies to convert organic fluorophores into red/near-infrared emitting analogues and their utilization in bioimaging probes

Organic fluorophores aided by current microscopy imaging modalities are essential for studying biological systems. Recently, red/near-infrared emitting fluorophores have attracted great research efforts, as they enable bioimaging applications with reduced autofluorescence interference and light scattering, two significant obstacles for deep-tissue imaging, as well as reduced photodamage and photobleaching. Herein, we analyzed the current strategies to convert key organic fluorophores bearing xanthene, coumarin, and naphthalene cores into longer wavelength-emitting derivatives by focussing on their effectiveness and limitations. Together, we introduced typical examples of how such fluorophores can be used to develop molecular probes for biological analytes, along with key sensing features. Finally, we listed several critical issues to be considered in developing new fluorophores.

Development of a Water-Soluble Fluorescent Probe Based on Natural Flavylium for Mercury(II) Ion Detection and Clinical Antidote Evaluation

The health hazard posed by Hg2+ makes it imperative to develop a fast and convenient means for detecting Hg2+ in water samples and living objects. While fluorescence sensing technology is considered a promising candidate, the poor water solubility and fluorescence quenching in aqueous solutions of most existing probes limit their practical application. To overcome this, we developed a natural flavylium-inspired fluorescent probe with excellent water solubility. Our probe demonstrated outstanding performance of high sensitivity (LOD = 0.47 nM), fast response (<10 min), and great selectivity for Hg2+. Notably, we validated its applicability in real water, urine samples, and living cells. Furthermore, the probe was successfully applied to evaluate the effectiveness of antidotes for clinical Hg2+ poisoning.

Acid and Hypoxia Tandem-Activatable Deep Near-Infrared Nanoprobe for Two-Step Signal Amplification and Early Detection of Cancer

The early detection of cancers can significantly change outcomes even with existing treatments. However, ~50% of cancers still cannot be detected until they reach an advanced stage, highlighting the great challenges in the early detection. Here, an ultrasensitive deep near-infrared (dNIR) nanoprobe that is successively responsive to tumor acidity and hypoxia is reported. It is demonstrated that the new nanoprobe specifically detects tumor hypoxia microenvironment based on deep NIR imaging in ten different types of tumor models using cancer cell lines and patient-tissue derived xenograft tumors. By combining the acidity and hypoxia specific two-step signal amplification with a deep NIR detection, the reported nanoprobe enables the ultrasensitive visualization of hundreds of tumor cells or small tumors with a size of 260 µm in whole-body imaging or 115 µm metastatic lesions in lung imaging. As a result, it reveals that tumor hypoxia can occur as early as the lesions contain only several hundred cancer cells.

Hypsochromic Shift Donor-Acceptor NIR-II Dye for High-Efficiency Tumor Imaging

Nowadays, second near-infrared window (NIR-II) dyes' development focuses on pursuing a longer absorption/emission wavelength and higher quantum yield, which usually means an extended π conjugation system, resulting in an enormous molecular weight and poor druggability. Most researchers thought that the reduced π conjugation system would bring on a blueshift spectrum that causes dim imaging qualities. Little efforts have been made to study smaller NIR-II dyes with a reduced π conjugation system. Herein, we synthesized a reduced π conjugation system donor-acceptor (D-A) probe TQ-1006 (Em = 1006 nm). Compared with its counterpart donor-acceptor-donor (D-A-D) structure TQT-1048 (Em = 1048 nm), TQ-1006 exhibited comparable excellent blood vessels, lymphatic drainage imaging performance, and a higher tumor-to-normal tissue (T/N) ratio. An RGD conjugated probe TQ-RGD showed an extra high contrast tumor imaging (T/N ≥ 10), further proving D-A dyes' excellent NIR-II biomedical imaging applications. Overall, the D-A framework provides a promising approach to designing next-generation NIR-II fluorophores.

Rigid and Photostable Shortwave Infrared Dye Absorbing/Emitting beyond 1200 nm for High-Contrast Multiplexed Imaging

The shortwave infrared (SWIR) spectral region beyond 1200 nm offers optimal tissue penetration depth and has broad potential in diagnosis, therapy, and surgery. Here, we devised a novel class of fluorochromic scaffold, i.e., a tetra-benzannulated xanthenoid (EC7). EC7 absorbs/emits maximally at 1204/1290 nm in CH₂Cl₂ and exhibits an unparalleled molar absorptivity of 3.91 × 10⁵ cm^-1 M^-1 and high transparency to light at 400-900 nm. It also exhibited high resistance toward both photobleaching and symmetry breaking due to its unique structural rigidity. It is feasible for in vivo bioimaging and particularly suitable to couple with the shorter-wavelength analogues for high-contrast multiplexing. High-contrast dual-channel intraoperative imaging of the hepatobiliary system and three-channel in vivo imaging of the intestine, the stomach, and the vasculature were showcased. EC7 is a benchmark fluorochrome for facile biomedical exploitation of the SWIR region beyond 1200 nm.

Xanthene-Based Nitric Oxide-Responsive Nanosensor for Photoacoustic Imaging in the SWIR Window

Shortwave infrared (SWIR) dyes are characterized by their ability to absorb light from 900 to 1400 nm, which is ideal for deep tissue imaging owing to minimized light scattering and interference from endogenous pigments. An approach to access such molecules is to tune the photophysical properties of known near-infrared dyes. Herein, we report the development of a series of easily accessible (three steps) SWIR xanthene dyes based on a dibenzazepine donor conjugated to thiophene (SCR-1), thienothiophene (SCR-2), or bithiophene (SCR-3). We leverage the fact that SCR-1 undergoes a bathochromic shift when aggregated for in vivo studies by developing a ratiometric nanoparticle for NO (rNP-NO), which we employed to successfully visualize pathological levels of nitric oxide in a drug-induced liver injury model via deep tissue SWIR photoacoustic (PA) imaging. Our work demonstrates how easily this dye series can be utilized as a component in nanosensor designs for imaging studies.

Red-to-Near-Infrared Emitting PyrrolylBODIPY Dyes: Synthesis, Photophysical Properties and Bioimaging Application

Near-infrared (NIR) fluorophores with characteristics such as deep tissue penetration, minimal damage to the biological samples, and low background interference, are highly sought-after materials for in vivo and deep-tissue fluorescence imaging. Herein, series of 3-pyrrolylBODIPY derivatives and 3,5-dipyrrolylBODIPY derivatives have been prepared by a facile regioselective nucleophilic aromatic substitution reaction (S_N Ar) on 3,5-halogenated BODIPY derivatives (3,5-dibromo or 2,3,5,6-tetrachloroBODIPYs) with pyrroles. The installation of a pyrrolic unit onto the 3-position of the BODIPY chromophore leads to a dramatic red shift of both the absorption (up to 160 nm) and the emission (up to 260 nm) in these resultant 3-pyrrolylBODIPYs with respect to that of the BODIPY chromophore. Their further 5-positional functionalization provides a facile way to fine tune their photophysical properties, and these resulting dipyrrolylBODIPYs and functionalized pyrrolylBODIPYs show strong absorption in the deep red-to-NIR regions (595-684 nm) and intense NIR fluorescence emission (650-715 nm) in dichloromethane. To demonstrate the applicability of these functionalized pyrrolylBODIPYs as NIR fluorescent probes for cell imaging, pyrrolylBODIPY 6 a containing mitochondrion-targeting butyltriphenylphosphonium cationic species was also prepared. It selectively localized in mitochondria of HeLa cells, with low cytotoxicity and intense deep red fluorescence emission.

A Space-Dependent 'Enzyme-Substrate' Type Probe based on 'Carboxylesterase-Amide Group' for Ultrafast Fluorescent Imaging Orthotopic Hepatocellular Carcinoma

Fast and selective fluorescence imaging for a biomarker to related-disease diagnosis remains a significant challenge due to complex physical environment. Human carboxylesterase (CE) is expected to be a potential biomarker of hepatocellular carcinoma (HCC) to improve the accuracy of diagnosis. However, existing probes for CE has slow response rate and low selectivity. Herein, the amide group is selected as CE-responsive sites based on the "substrate-hydrolysis enzymatic reaction" approach. From a series of off-on probes with leave groups in the amide unit, probe J_Fast is screened with the optimal combination of rapid response rate and high selectivity toward CE. J_Fast requires only 150 s to reach the maximum fluorescence at 676 nm in the presence of CE and free from the interference of other esterase. Computational docking simulations indicate the shortest distance between the CE and active site of J_Fast . Cell and in vivo imaging present that the probe can turn on the liver cancer cells and tumor region precisely. Importantly, J_Fast is allowed to specifically image orthotopic liver tumor rather than metastatic tumor and distinguish human primary liver cancer tissue from adjacent ones. This study provides a new tool for CE detection and promotes advancements in accurate HCC diagnosis.

Rational Design of Polymethine Dyes with NIR-II Emission and High Photothermal Conversion Efficiency for Multimodal-Imaging-Guided Photo-Immunotherapy

Phototheranostics have emerged and flourished as a promising pattern for cancer theranostics owing to their precise photoinduced diagnosis and therapeutic to meet the demands of precision medicine. The diagnosis information and therapeutic effect are directly determined by the fluorescence imaging ability and photothermal conversion efficiency (PCE) of phototheranostic agents. Hence, how to balance the competitive radiative and nonradiative processes of phototheranostic agents is the key factor to evaluate the phototheranostic effect. Herein, molecules named ICRs with high photostaibility  are rationally designed, exhibiting fluorescence emission in the second near-infrared window (NIR-II, 1000-1700 nm) and high PCE, which are related to the strong donor-acceptor (D-A) interaction and high reorganization energy Noteworthily, ICR-Qu with stronger D-A interaction and a large-sized conjugated unit encapsulated in nanoparticles exhibits high PCE (81.1%). In addition, ICR-QuNPs are used for fluorescence imaging (FLI), photoacoustic imaging (PAI), and photothermal imaging (PTI) to guide deep-tissue photonic hyperthermia, achieving precise removal and inhibition of breast cancer. Furthermore, combined with α-PD-1, ICR-QuNPs show huge potential to be a facile and efficient tool for photo-immunotherapy. More importantly, this study not only reports an "all-in-one" polymethine-based phototheranostic agent, but also sheds light on the exploration of versatile organic molecules for future practical applications.

Single-molecule characterization of a bright and photostable deep-red fluorescent squaraine-figure-eight (SF8) dye

Squaraine Figure Eight (SF8) dyes are a unique class of deep-red fluorescent dyes with self-threaded molecular architecture that provides structural rigidity while simultaneously encapsulating and protecting the emissive fluorochrome. Previous cell microscopy and bulk phase studies of SF8 dyes indicated order of magnitude enhancements in photostability over conventional pentamethine cyanine dyes such as Cy5. Studies conducted at the single molecule level now reveal that these ensemble level enhancements carry over to the single molecule level in terms of enhanced emission quantum yields, longer times to photobleaching, and enhanced total photon yields. When compared to Cy5, the SF8-based dye SF8(D4)2 possesses a three-fold larger single molecule emission quantum yield, exhibits order of magnitude longer average times before photobleaching, and exhibits twenty times larger photon yields. Additional features such as water solubility, fluorochrome encapsulation to protect it against nucleophilic attack, and selective biomarker targeting capability make SF8-based dyes promising candidates for biological labeling and microscopy applications and single molecule tracking.

Recent progress of second near-infrared (NIR-II) fluorescence microscopy in bioimaging

Visualizing biological tissues in vivo at a cellular or subcellular resolution to explore molecular signaling and cell behaviors is a crucial direction for research into biological processes. In vivo imaging can provide quantitative and dynamic visualization/mapping in biology and immunology. New microscopy techniques combined with near-infrared region fluorophores provide additional avenues for further progress in vivo bioimaging. Based on the development of chemical materials and physical optoelectronics, new NIR-II microscopy techniques are emerging, such as confocal and multiphoton microscopy, light-sheet fluorescence microscopy (LSFM), and wide-field microscopy. In this review, we introduce the characteristics of in vivo imaging using NIR-II fluorescence microscopy. We also cover the recent advances in NIR-II fluorescence microscopy techniques in bioimaging and the potential for overcoming current challenges.

Activity-Based Sensing for Chemistry-Enabled Biology: Illuminating Principles, Probes, and Prospects for Boronate Reagents for Studying Hydrogen Peroxide

Activity-based sensing (ABS) offers a general approach that exploits chemical reactivity as a method for selective detection and manipulation of biological analytes. Here, we illustrate the value of this chemical platform to enable new biological discovery through a case study in the design and application of ABS reagents for studying hydrogen peroxide (H2O2), a major type of reactive oxygen species (ROS) that regulates a diverse array of vital cellular signaling processes to sustain life. Specifically, we summarize advances in the use of activity-based boronate probes for the detection of H2O2 featuring high molecular selectivity over other ROS, with an emphasis on tailoring designs in chemical structure to promote new biological principles of redox signaling.

The pursuit of xanthenoid fluorophores with near-infrared-II emission for in vivo applications

As fluorescence imaging in the second near-infrared window (NIR-II, 1000-1700 nm) has gained increasing attention, it is inevitable that NIR-II fluorophores, the cornerstone of NIR-II imaging, have come to the middle of the stage. NIR-II xanthenoid fluorophores with good stability, high brightness, and fluorescence adjustability are becoming popular. We here reviewed the recent progress of xanthenoid fluorophores with NIR-II emission for in vivo applications. Especially, we focus on the strategies used for longer wavelength and fluorescence regulation to construct OFF-ON or ratiometric NIR-II fluorescent probes.