Effects of Amino Group Substitution on the Photophysical Properties and Stability of Near-Infrared Fluorescent P-Rhodamines

Near-infrared fluorescent HaloTag ligands for efficient organelle labelling in live cells

A series of HaloTag ligands that incorporate near-infrared (NIR)-emissive phospha-rhodamine (POR) dyes have been developed. The PORs that contain dealkylated amino groups exhibit a hypsochromic shift in their absorption and emission wavelengths. Subsequent refinement of the POR spirocyclization equilibrium significantly enhanced membrane permeability, thereby leading to a substantial reduction in the time necessary for labelling. Consequently, target organelles could even be labeled at low POR dye concentrations in the tens of nM range.

Synthesis and Photodynamic Activities of Pyridine- or Pyridinium-Substituted Aza-BODIPY Photosensitizers

In this work, various novel pyridinyl- and pyridinium-modified Aza-BODIPY PSs were designed and constructed based on monoiodo Aza-BODIPY PSs (BDP-4 and BDP-15) in an attempt to construct "structure-inherent organelles-targeted" PSs to endow potential organelle-targeting ability. Pyridinyl PSs displayed potent photodynamic efficacy, and monorigidified PSs were very effective. The monorigidified PS 20 with meta-pyridinyl moiety displayed the most potent photoactivity and negligible dark toxicity with a favorable dark/phototoxicity ratio (>4800). To our surprise, monorigidified PS with meta-pyridinyl moiety (e.g., 20) was lipid droplet-targeted. 20 showed good cellular uptake and intracellular ROS generation compared with BDP-15. The preliminary cell death process exploration indicated that 20 resulted in lipid peroxidation and induced cell death through an iron-independent ferroptosis-like cell death pathway. In vivo antitumor efficacy experiments manifested that 20 significantly inhibited tumor growth and outperformed BDP-15 and Ce6 even under a single low-dose light irradiation (30 J/cm2).

Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging

The development of near-infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha-rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2-carboxy-3-benzothiophenyl group at the 9-position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X-ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non-specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag-fused proteins, enabling the long-term imaging of cell division and the 5-color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR-emissive properties, multi-color time-lapse super-resolution 3D imaging, namely super-resolution 5D-imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells.

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.

Novel Method for the Synthesis of Merocyanines: New Photophysical Possibilities for a Known Class of Fluorophores

A new, transformative method for the preparation of rhodols and other merocyanines from readily available tetrafluorohydroxybenzaldehyde and aminophenols has been developed. It is now possible to prepare merocyanines bearing three fluorine atoms and additional conjugated rings, and the whole one-pot process occurs under neutral, mild conditions. Three heretofore unknown merocyanine-based architectures were prepared using this strategy from aminonaphthols and 4-hydroxycoumarins. The ability to change the structure of original rhodol chromophore into π-expanded merocyanines translates to a comprehensive method for the modulation of photophysical properties, such as shifting the absorption and emission bands across almost the entire visible spectrum, reaching a huge Stokes shift i. e. 4800 cm-1 , brightness approximately 80.000 M-1  cm-1 , two-photon absorption cross-section above 150 GM and switching-on/off solvatofluorochromism. A detailed investigation allowed to rationalize the different spectroscopic behavior of rhodols and new merocyanines, addressing solvatochromism and two-photon absorption.

Fluorene analogues of xanthenes - low molecular weight near-infrared dyes

Fluorene-based analogues of fluorescein, rhodol, and rhodamine exhibit absorption and fluorescence beyond 800-900 nm in water, 300-400 nm red-shifted compared to the original oxygen-bridged xanthene dyes, giving potential access to low molecular weight fluorescent markers for the second biological window (NIR-II, ca. 1000-1350 nm).

Electron-Deficient Heteroacenes that Contain Two Boron Atoms: Near-Infrared Fluorescence Based on a Push-Pull Effect*

Electron-deficient heteroacenes that contain two tricoordinate boron atoms in their acene skeletons and planarized phenyl ether moieties at their periphery were synthesized via the borylation of silicon-bridged precursors. X-ray crystallographic analysis revealed quinoidal structures, which give rise to two-step reversible redox processes for both the reduction and oxidation. These compounds exhibit intense absorption and sharp fluorescence bands with vibronic structures in the near-infrared (NIR) region. These properties originate from the push-pull effect along the long axis of the molecule derived from the electron-donating ether moieties and the electron-accepting boron moieties. Of particular note is the NIR emission of the thienothiophene-centered heteroacene, which has a maximum at 952 nm with a narrow band width of 309 cm^-1 in cyclohexane. A Franck-Condon analysis revealed the crucial role of the sterically less-hindered thienothiophene spacer in achieving this sharp emission band.

Late-stage functionalisation of alkyne-modified phospha-xanthene dyes: lysosomal imaging using an off-on-off type of pH probe

Near-infrared (NIR) fluorescent molecules are of great importance for the visualisation of biological processes. Among the most promising dye scaffolds for this purpose are P[double bond, length as m-dash]O-substituted phospha-xanthene (POX) dyes, which show NIR emission with high photostability. Their practical utility for in vitro and in vivo imaging has recently been demonstrated. Although classical modification methods have been used to produce POX-based fluorescent probes, it is still a challenge to introduce additional functional groups to control the localisation of the probe in cells. Herein, we report on the development of POXs that bear a 4-ethynylphenyl group on the phosphorus atom. These dyes can subsequently be functionalised with azide-tagged biomolecules via a late-stage Cu-catalysed azide/alkyne cycloaddition (CuAAC) reaction, thus achieving target-selective labelling. To demonstrate the practical utility of the functionalised POXs, we designed a sophisticated NIR probe that exhibits a bell-shaped off-on-off pH-response and is able to assess the degree of endosomal maturation.