The Dynamic Range of Acidity: Tracking Rules for the Unidirectional Penetration of Cellular Compartments.

Labeled ammonium cations with pKa ∼7.4 accumulate in acidic organelles because they can be neutralized transiently to cross the membrane at cytosolic pH 7.2 but not at their internal pH<5.5. Retention in early endosomes with less acidic internal pH was achieved recently using weaker acids of up to pKa 9.8. We report here that primary ammonium cations with higher pKa 10.6, label early endosomes more efficiently. This maximized early endosome tracking coincides with increasing labeling of Golgi networks with similarly weak internal acidity. Guanidinium cations with pKa 13.5 cannot cross the plasma membrane in monomeric form and label the plasma membrane with selectivity for vesicles embarking into endocytosis. Self-assembled into micelles, guanidinium cations enter cells like arginine-rich cell-penetrating peptides and, driven by their membrane potential, penetrate mitochondria unidirectionally despite their high inner pH. The resulting tracking rules with an approximated dynamic range of pKa change ∼3.5 are expected to be generally valid, thus enabling the design of chemistry tools for biology research in the broadest sense. From a practical point of view, most relevant are two complementary fluorescent flipper probes that can be used to image the mechanics at the very beginning of endocytosis.

Photocleavable Fluorescent Membrane Tension Probes: Fast Release with Spatiotemporal Control in Inner Leaflets of Plasma Membrane, Nuclear Envelope, and Secretory Pathway.

Mechanosensitive flipper probes are attracting interest as fluorescent reporters of membrane order and tension in biological systems. We introduce PhotoFlippers, which contain a photocleavable linker and an ultralong tether between mechanophore and various targeting motifs. Upon irradiation, the original probe is released and labels the most ordered membrane that is accessible by intermembrane transfer. Spatiotemporal control from photocleavable flippers is essential to access open, dynamic or elusive membrane motifs without chemical or physical interference. For instance, fast release with light is shown to place the original small-molecule probes into the innermost leaflet of the nuclear envelope to image changes in membrane tension, at specific points in time of membrane trafficking along the secretory pathway, or in the inner leaflet of the plasma membrane to explore membrane asymmetry. These results identify PhotoFlippers as useful chemistry tools to enable research in biology.

Flipper Probes for the Community.

This article describes four fluorescent membrane tension probes that have been designed, synthesized, evaluated, commercialized and applied to current biology challenges in the context of the NCCR Chemical Biology. Their names are Flipper-TR®, ER Flipper-TR®, Lyso Flipper-TR®, and Mito Flipper-TR®. They are available from Spirochrome.

Fluorescent Membrane Tension Probes for Early Endosomes.

Fluorescent flipper probes have been introduced recently to image membrane tension in live cells, and strategies to target these probes to specific membranes are emerging. In this context, early endosome (EE) targeting without the use of protein engineering is especially appealing because it translates into a fascinating transport problem. Weakly basic probes, commonly used to track the inside of acidic late endosomes and lysosomes, are poorly retained in EE because they are sufficiently neutralized in weakly acidic EE, thus able to diffuse out. Here, we disclose a rational strategy to target EE using a substituted benzylamine with a higher pKa value as a head group of the flipper probe. The resulting EE flippers are validated for preserved mechanosensitivity, ready for use in biology, particularly to elucidate the mechanics of endocytosis.

Surface-Confined Macrocyclization via Dynamic Covalent Chemistry.

Surface-confined synthesis is a promising approach to build complex molecular nanostructures including macrocycles. However, despite the recent advances in on-surface macrocyclization under ultrahigh vacuum, selective synthesis of monodisperse and multicomponent macrocycles remains a challenge. Here, we report on an on-surface formation of [6 + 6] Schiff-base macrocycles via dynamic covalent chemistry. The macrocycles form two-dimensional crystalline domains on the micrometer scale, enabled by dynamic conversion of open-chain oligomers into well-defined ∼3.0 nm hexagonal macrocycles. We further show that by tailoring the length of the alkyl substituents, it is possible to control which of three possible products-oligomers, macrocycles, or polymers-will form at the surface. In situ scanning tunneling microscopy imaging combined with density functional theory calculations and molecular dynamics simulations unravel the synergistic effect of surface confinement and solvent in leading to preferential on-surface macrocyclization.

Dithienothiophenes at Work: Access to Mechanosensitive Fluorescent Probes, Chalcogen-Bonding Catalysis, and Beyond.

In this review, the multifunctionality of dithieno[3,2-b:2',3'-d]thiophenes (DTTs) is covered comprehensively. This is of interest because all involved research is very recent and emphasizes timely topics such as mechanochemistry for bioimaging or chalcogen bonds for catalysis and solar cells and because the newly emerging privileged scaffold is embedded in an inspiring structural space. At the beginning, DTTs are introduced with regard to nomenclature, constitutional isomers, and optoelectronic properties. The structural space around DTTs is mapped out next with regard to heteroatom substitution in the bridge and core, covering much of the periodic table, eccentric heteroatom doping, and bridge expansions. After a brief summary of synthetic approaches to the DTT scaffold, chalcogen bonds are introduced as, together with redox switching and turn-on fluorescence, one of the three conceptual foundations of the most multifunctionality. Realized functions cover anion binding, transport (ion carriers, ion channels), catalysis, and the first fluorescent probes to image physical forces in living cells. The appearance of DTTs in many other photosystems covers push-pull systems for nonlinear optics and dye-sensitized solar cells, DTT polymers in light-emitting diodes, organic field-effect transistors and organic photovoltaics, DTT self-assembly and templated assembly into thin films and fluorescent fibers, also within cells, and the integration of DTTs into photochromes and biaromatics that violate the Hückel rule..