Improving the Brightness of Pyronin Fluorophore Systems through Quantum-Mechanical Predictions.

The pyronin class of fluorophores serves a critical role in numerous imaging applications, particularly involving preferential staining of RNA through base pair intercalation. Despite this important role in molecular staining applications, the same set of century-old pyronins (i.e.

Synthesis of a fluorinated pyronin that enables blue light to rapidly depolarize mitochondria.

Fluorinated analogues of the fluorophore pyronin B were synthesized as a new class of amine-reactive drug-like small molecules. In water, 2,7-difluoropyronin B was found to reversibly react with primary amines to form covalent adducts. When this fluorinated analogue is added to proteins, these adducts undergo additional oxidation to yield fluorescent 9-aminopyronins.

Synthesis of Rhodamines and Rosamines Using 3,6-Difluoroxanthone as a Common Intermediate.

Rhodamines and structurally similar rosamines are some of the most highly utilized tools for molecular imaging experiments. We report a general and high-yielding route to produce 18 examples of rhodamines and rosamines, including tetramethylrhodamine, rhodamine B, and Janelia Fluor 549, from a single xanthone intermediate, 3,6-difluoroxanthone. Spectroscopic studies revealed trends in fluorophore efficiency based on substitution patterns at the 3'-, 6'-, and 9'-positions, providing insights to aid future designs of rhodamines/rosamines.

Synthesis of pH Dependent Pyrazole, Imidazole, and Isoindolone Dipyrrinone Fluorophores using a Claisen-Schmidt Condensation Approach.

Methine-bridged conjugated bicyclic aromatic compounds are common constituents of a range of biologically relevant molecules such as porphyrins, dipyrrinones, and pharmaceuticals. Additionally, restricted rotation of these systems often results in highly to moderately fluorescent systems as observed in 3H,5H-dipyrrolo[1,2-c:2',1'-f]pyrimidin-3-ones, xanthoglows, pyrroloindolizinedione analogs, BODIPY analogs, and the phenolic and imidazolinone ring systems of Green Fluorescent Protein (GFP). This manuscript describes an inexpensive and operationally simple method of performing a Claisen-Schmidt condensation to generate a series of fluorescent pH dependent pyrazole/imidazole/isoindolone dipyrrinone analogs.

Tautomycetin Synthetic Analogues: Selective Inhibitors of Protein Phosphatase I.

Ser/Thr protein phosphatases (PPs) regulate a substantial range of cellular processes with protein phosphatases 1 (PP1) and 2 A (PP2A) accounting for over 90 % of the activity within cells. Nevertheless, tools to study PPs are limited as PPs inhibitors, particularly those selective for PP1 inhibition, are relatively scarce. Two examples of PP1-selective inhibitors, which share structural similarities, are tautomycin (TTM) and tautomycetin (TTN).

Pyrazole, Imidazole, and Isoindolone Dipyrrinone Analogues: pH-Dependent Fluorophores That Red-Shift Emission Frequencies in a Basic Solution.

Dipyrrinones are nonfluorescent yellow-pigmented constituents of bilirubin that undergo Z to E isomerization when excited with UV/blue light. Mechanical restriction of the E/Z isomerization process results in highly fluorescent compounds such as ,-methylene-bridged dipyrrinones and xanthoglows. This manuscript describes the first examples of dipyrrinone analogues, which exhibit fluorescence without covalently linking the pyrole-pyrrolidine nitrogen atoms.

A General Method for Nucleophilic Aromatic Substitution of Aryl Fluorides and Chlorides with Dimethylamine using Hydroxide-Assisted Decomposition of N,N-Dimethylforamide.

A practical and convenient procedure for the nucleophilic aromatic substitution of aryl fluorides and chlorides with dimethylamine was developed using a hydroxide assisted, thermal decomposition of N,N-dimethylforamide. These conditions are tolerant of nitro, nitrile, aldehyde, ketone, and amide groups but will undergo acyl substitution to form amides for methyl esters and acyl chlorides. Isolated yields of the products range from 44 - 98%, with the majority being greater than 70% for seventeen examples.

Synthesis of a Fluorescent Acridone using a Grignard Addition, Oxidation, and Nucleophilic Aromatic Substitution Reaction Sequence.

A three-pot synthesis oriented for an undergraduate organic chemistry laboratory was developed to construct a fluorescent acridone molecule. This laboratory experiment utilizes Grignard addition to an aldehyde, alcohol oxidation, and iterative nucleophilic aromatic substitution steps to produce the final product. Each of the intermediates and the acridone product of the synthesis are analyzed by common techniques available in most undergraduate chemistry laboratories, such as melting point, TLC, IR spectroscopy, UV-Vis spectroscopy, and fluorescence spectroscopy.

Efficient and Scalable Synthesis of 4-Carboxy-Pennsylvania Green Methyl Ester: A Hydrophobic Building Block for Fluorescent Molecular Probes.

Fluorinated fluorophores are valuable tools for studies of biological systems. However, amine-reactive single-isomer derivatives of these compounds are often very expensive. To provide an inexpensive alternative, we report a practical synthesis of 4-carboxy-Pennsylvania Green methyl ester.

Detection of protein-protein interactions by proximity-driven S(N)Ar reactions of lysine-linked fluorophores.

Critical protein-protein interactions are ubiquitous in biology. To provide a new method to detect these interactions, we designed and synthesized fluorinated bromopyronins as molecular probes. These electrophilic compounds rapidly react with amines via a S(N)Ar mechanism to form modestly electrophilic aminopyronin fluorophores.

Novel acid-activated fluorophores reveal a dynamic wave of protons in the intestine of Caenorhabditis elegans.

Unlike the digestive systems of vertebrate animals, the lumen of the alimentary canal of Caenorhabditis elegans is unsegmented and weakly acidic (pH ~4.4), with ultradian fluctuations to pH > 6 every 45-50 s. To probe the dynamics of this acidity, we synthesized novel acid-activated fluorophores termed Kansas Reds.

Synthesis of fluorinated benzophenones, xanthones, acridones, and thioxanthones by iterative nucleophilic aromatic substitution.

Fluorination of fluorophores can substantially enhance their photostability and improve spectroscopic properties. To facilitate access to fluorinated fluorophores, bis(2,4,5-trifluorophenyl)methanone was synthesized by treatment of 2,4,5-trifluorobenzaldehyde with a Grignard reagent derived from 1-bromo-2,4,5-trifluorobenzene, followed by oxidation of the resulting benzyl alcohol. This hexafluorobenzophenone was subjected to sequential nucleophilic aromatic substitution reactions, first at one or both of the more reactive 4,4'-fluorines, and second by cyclization through substitution of the less reactive 2,2'-fluorines, using a variety of oxygen, nitrogen, and sulfur nucleophiles, including hydroxide, methoxide, amines, and sulfide.

Synthesis and hepatic transport of strongly fluorescent cholephilic dipyrrinones.

A new class of highly fluorescent (phi(F) 0.3-0.8) low molecular weight water-soluble cholephilic compounds has been synthesized in two steps from dipyrrinones.