Site-Specific Turn-On Fluorescent Labeling of DNA-Interacting Protein Using Oligodeoxynucleotides That Modify Lysines To Produce 5,6-Dimethoxy 3-Methyleneisoindolin-1-one

Photo-caged 2-butene-1,4-dial as an efficient, target-specific photo-crosslinker for covalent trapping of DNA-binding proteins

Covalent trapping of DNA-binding proteins via photo-crosslinking is an advantageous method for studying DNA-protein interactions. However, traditional photo-crosslinkers generate highly reactive intermediates that rapidly and non-selectively react with nearby functional groups, resulting in low target-capture yields and high non-target background capture. Herein, we report that photo-caged 2-butene-1,4-dial (PBDA) is an efficient photo-crosslinker for trapping DNA-binding proteins. Photo-irradiation (360 nm) of PBDA-modified DNA generates 2-butene-1,4-dial (BDA), a small, long-lived intermediate that reacts selectively with Lys residues of DNA-binding proteins, leading in minutes to stable DNA-protein crosslinks in up to 70% yield. In addition, BDA exhibits high specificity for target proteins, leading to low non-target background capture. The high photo-crosslinking yield and target specificity make PBDA a powerful tool for studying DNA-protein interactions.

Supramolecular Phthalimide Networks Via Tandem Diels-Alder Reaction-Aromatization Using Biomass-Derived Furanic Dienes

The design and synthesis of phthalimide derivatives are important goals for applications in fields such as pharmaceutical science and optoelectronics. In the present study, a facile and convenient synthetic pathway (no heat or acid/catalyst needed) is devised to produce phthalimides from a biomass-derived furan by directly introducing an N-carbamate group at the C-2 position of the furan ring via thermal Curtius rearrangement. The electron-donating N-carbamate group increases the energy level of the highest occupied molecular orbital of the furan diene, resulting in a significant increase of the rate of the Diels-Alder reaction with maleimide compared to the conventional furfuryl furan. Interestingly, the Diels-Alder adduct smoothly undergoes aromatization (dehydration) to generate the phthalimide motif. It is shown that the biomass-derived phthalimides can produce supramolecular gels and act as sensors of basic anions like F^- and CN^- . The novel synthetic pathway to phthalimide derivatives from a biomass-derived furan can potentially be used to develop novel phthalimide motifs for a variety of applications.

Beyond conventional construction of the phthalimide core: a review

This review highlights (2010–2021) different strategies for the construction of the phthalimide core apart from traditional synthetic routes.

Synthesis of phthalimides cross-conjugated with an azulene ring, and their structural, optical and electrochemical properties

The preparation of phthalimides cross-conjugated with an azulene ring was established by a one-pot Diels-Alder reaction of the corresponding 2-aminofuran derivatives with several maleimides, without the isolation of the intermediately formed [4 + 2] cycloadducts. The structure, optical and electrochemical properties of the novel phthalimide derivatives were clarified by single-crystal X-ray analysis, UV/Vis and fluorescence spectra, spectroelectrochemistry and voltammetry experiments, and theoretical calculations. These results indicated that the substituents on the azulene ring greatly affect the optical and electrochemical properties of the molecules.

A light-responsive, self-immolative linker for controlled drug delivery via peptide- and protein-drug conjugates

Photoirradiation of the PC4AP linker generates an active intermediate that reacts intramolecularly with a primary amine on the carrier peptide/protein, leading to rapid release of the drug without generating any toxic side products.

When designing prodrugs, choosing an appropriate linker is the key to achieving efficient, controlled drug delivery. Herein, we report the use of a photocaged C4′-oxidized abasic site (PC4AP) as a light-responsive, self-immolative linker. Any amine- or hydroxyl-bearing drug can be loaded onto the linker via a carbamate or carbonate bond, and the linker is then conjugated to a carrier peptide or protein via an alkyl chain. The PC4AP linker is stable under physiologically relevant conditions. However, photodecaging of the linker generates an active intermediate that reacts intramolecularly with a primary amine (the ε-amine of a lysine residue and the N-terminal amine) on the carrier, leading to rapid and efficient release of the drug via an addition–elimination cascade, without generating any toxic side products. We demonstrated that the use of this self-immolative linker to conjugate the anticancer drug doxorubicin to a cell-penetrating peptide or an antibody enabled targeted, controlled delivery of the drug to cells. Our results suggest that the linker can be used with a broad range of carriers, such as cell-penetrating peptides, proteins, antibodies, and amine-functionalized polymers, and thus will find a wide range of practical applications.

Synthesis of azulenophthalimides by phosphine-mediated annulation of 1,2-diformylazulenes with maleimides

The reaction of 1,2-diformylazulene with maleimides in the presence of PPh₃ gave the azulenophthalimides. The optical and electrochemical properties of the azulenophthalimides were investigated.

7-Hydroxy-3-methyleneisoindolin-1-one as a New ESIPT-Fluorescent Probe to Monitor Aqueous Environments

A 7-hydroxy derivative of 3-methyleneisoindolin-1-one 1 was synthesized and its properties as a new fluorophore undergoing excited-state intramolecular proton transfer (ESIPT) were investigated. In alcohols and dimethylsulfoxide, 1 exhibited dual emission at ca. 380 and 525-540 nm when excited at ca. 336 nm, which agreed well with the density functional theory (DFT) and time-dependent (TD)-DFT-calculated emission predictions of 1 and its ESIPT tautomer. In aqueous solutions at near neutral pH, 1 exhibited a broad emission band at ca. 497 nm, presumably caused by the overlap of emissions from 1 and the excited state phenolate species of 1. In binary mixtures of H₂O and EtOH, the wavelength and intensity of fluorescence maxima were dependent on the dielectric constant of the solvent, suggesting that 1 could be applied as a fluorescent probe to monitor aqueous environments.

Thiol Specific and Tracelessly Removable Bioconjugation via Michael Addition to 5-Methylene Pyrrolones

5-Methylene pyrrolones (5MPs) are highly thiol-specific and tracelessly removable bioconjugation tools. 5MPs are readily prepared from primary amines in one step. 5MPs exhibit significantly improved stability under physiologically relevant conditions and cysteine specificity compared to commonly used analogues, maleimides. Michael addition of thiol to 5MPs occurs rapidly, cleanly, and does not generate a stereocenter. The conjugates efficiently release thiols via retro-Michael reaction in alkaline buffer (pH 9.5) or via thiol exchange at pH 7.5. This unique property makes 5MPs valuable for the controlled release of conjugated cargo and temporary thiol protection. The utilization of 5MPs for protein immobilization and pull-down of active complexes is illustrated using E. coli. acetohydroxyacid synthase isozyme I.

Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking

Porphyrin-based photosensitisers and their DNA conjugates have been evaluated for interstrand crosslink generation using furan containing oligonucleotides and red light.