Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications

The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.

This minireview describes the development of NIR chemical probes for various protein-tag systems.     

The fifth overtones of the C-H stretching vibrations and the bond lengths in some heterocyclic compounds

The fifth overtones of the C-H stretching vibrations of pyridine, pyrazine, thiophene, 3-methylthiophene, furan and pyrrole in the liquid state have been observed by a thermal lens technique. It was found that their frequency shifts from that of benzene are proportional to the decrease in the relevant C-H bond length.     

Fluorogenic probes for detecting deacylase and demethylase activity towards post-translationally-modified lysine residues

Reversible enzymatic post-translational modification of the ε-amino groups of lysine residues (e.g. N-acylation reactions) plays an important role in regulating the cellular activities of numerous proteins. This study describes how enzyme catalyzed N-deprotection of lysine residues of non-fluorescent peptide-coumarin probes can be used to generate N-deprotected peptides that undergo spontaneous O- to N-ester transfer reactions (uncatalyzed) to generate a highly fluorescent N-carbamoyl peptide. This enables detection of enzyme catalyzed N-deacetylation, N-demalonylation, N-desuccinylation and N-demethylation reactions activities towards the N-modified lysine residues of these probes using simple ‘turn on’ fluorescent assays.

We developed “turn-on” fluorescent probes that detect enzymatic lysine deacylation and demethylation critical for epigenetic and other cellular phenomena, using intramolecular O- to N-ester transfer reactions.     

Synthesis and inversion barriers of undeca- and dodeca-substituted saddle shaped porphyrin complexes

Synthesis and barriers to inversion of a series of highly saddle shaped complexes are reported. The ΔG^≠ has decreased by 8 kJ mol⁻¹ at 243 K when the meso phenyl groups are replaced by bulkier 2,6-dichlorophenyl groups, and by 17 kJ mol⁻¹ when one of the peripheral ethyl groups is removed.     

Laser photolysis studies of the photochemical reactions of chromium(III) octaethylporphyrin and tetramesitylporphyrin complexes in toluene solution

A nanosecond laser photolysis study was carried out for the Cr(III) porphyrin complexes of 2,3,7,8,12,13,17,18-octaethylporphyrin, [Cr(OEP)(Cl)(L)], and of 5,10,15,20-tetramesitylporphyrin, [Cr(TMP)(Cl)(L)], in toluene containing water and an excess amount of L (L = axial ligand). The laser photolysis generates the triplet excited state of the parent complex as well as a five-coordinate complex, [Cr(porphyrin)(Cl)], produced by the photodissociation of the axial ligand L. The yields for the formation of the triplet state and the photodissociation of L are found to markedly depend on the nature of both L and porphyrin ligand. The five-coordinate [Cr(porphyrin)(Cl)] readily reacts with both H(2)O and L in the bulk solution to give [Cr(porphyrin)(Cl)(H(2)O)] and [Cr(porphyrin)(Cl)(L)], respectively. The axial H(2)O ligand in [Cr(porphyrin)(Cl)(H(2)O)] is then substituted by the ligand L to regenerate the original complex [Cr(porphyrin)(Cl)(L)]. In principle, the substitution reaction takes place by the dissociative mechanism: the first step is the dissociation of H(2)O from [Cr(porphyrin)(Cl)(H(2)O)], followed by the reaction of the five-coordinate [Cr(porphyrin)(Cl)] with the ligand L to regenerate [Cr(porphyrin)(Cl)(L)]. The rate constants for this ligand substitution reaction are found to exhibit bell-shaped ligand concentration dependence. The detailed kinetic analysis revealed that both ligands L and H(2)O in toluene make a hydrogen bond with the axial H(2)O ligand in [Cr(porphyrin)(Cl)(H(2)O)] to yield dead-end complexes for the substitution reaction. The reaction mechanisms are discussed on the basis of the substituent effects of the porphyrin peripheral groups and the kinetic parameters determined from the temperature dependence of the rate constants.     

Concise synthesis of pyrrolophenanthridine alkaloids using a Pd-mediated biaryl coupling reaction with regioselective C-H activation via the intramolecular coordination of the amine to Pd

The concise synthesis of Amaryllidaceae alkaloids, such as anhydrolycorinone, anhydrolycorin-7-one, assoanine, and oxoassoanine, which have a pyrrolophenanthridine skeleton, was achieved in moderate yield using the Pd-mediated biaryl coupling reaction of 1-(2-halobenzyl)-2,3-dihydroindole, which applied the regioselective C-H activation method with intramolecular coordination of the benzylamino group to Pd.     

Product analyses and crosslink mechanism of plasma-polymerized methyl methacrylate

Plasma-polymerized methyl methacrylate (PPMMA) film was produced by a radio-frequency glow discharge of methyl methacrylate (MMA) gas with argon. PPMMA deposited under a plasma of mild energy was separated into a soluble fraction (sol-PPMMA) and an insoluble matrix (insol-PPMMA), which is highly crosslinked, by solvent-extraction and filtration. The chemical structure of the sol-PPMMA was determined by pyrolysis/gas chromatography, IR spectroscopy, ¹H-NMR, ¹³C-NMR, and elemental analysis techniques. On the other hand, the structure of the insol-PPMMA was examined with IR spectroscopy, ¹³C-NMR with CP/MAS method, and elemental analysis. The crosslinking mechanism in the plasma polymerization of MMA is discussed on the basis of product analyses of the sol-PPMMA and the insol-PPMMA.