Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Investigation of the Vibrational Characteristics of 6-Isocyano-1-Methyl-1H-Indole: Utilizing the Isonitrile Group as an Infrared Probe

Indole derivatives have garnered considerable attention in the realm of biochemistry due to their multifaceted properties. In this study, we undertake a systematic investigation of the vibrational characteristics of a model indole derivative, 6-isocyano-1-methyl-1H-indole (6ICMI), by employing a combination of FTIR, IR pump-probe spectroscopy, and theoretical calculations. Our findings demonstrate a strong dependence of the isonitrile stretching frequency of 6ICMI on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when the isonitrile group is bonded to aromatic groups. Both experimental and theoretical analyses unveil a significant correlation between the isonitrile stretch vibration of 6ICMI and the solvent acceptor number of alcohols. Furthermore, the polarization-controlled infrared pump-probe conducted on 6ICMI in dimethyl sulfoxide provides additional support for the potential use of the isonitrile stretching mode of 6ICMI as an effective infrared probe for local environments.

Ratiometric Fluorescent Hydrogel Test Kit for On-Spot Visual Detection of Nitrite

In this work, we proposed a new method based on carbon dots (named m-CDs) for selective and efficient detection of nitrite (NO₂^-), which was based on the interaction between the amine group of m-CDs and NO₂^- via a diazo reaction that produced diazonium salts and induced the fluorescence quenching of m-CDs. The concentration of NO₂^- shows a good linear relationship with a quenched fluorescence intensity from 0.063 to 2.0 μM ( R² = 0.996) with a detection limit of 0.018 μM. In addition, a ratiometric fluorescence probe ( m-CDs@[Ru(bpy)₃]²⁺) was constructed via electrostatic interaction by introducing Ru(bpy)₃Cl₂·6H₂O as an internal reference fluorescent reagent. Interestingly, a transition of the fluorescent color of the ratiometric probe from cyan to red could be visually observed upon increasing the concentration of NO₂^-. Based on these findings, a ratiometric fluorescent-based portable agarose hydrogel test kit was fabricated and applied for on-spot assessment of NO₂^- content within 10 min. As far as we know, this is the first ratiometric fluorescent sensor for visual detection of NO₂^-. It has broad application prospects in environmental monitoring and food safety assessment.

Isonitrile-Derivatized Indole as an Infrared Probe for Hydrogen-Bonding Environments

The isonitrile (NC) group has been shown to be a promising infrared probe for studying the structure and dynamics of biomolecules. However, there have been no systematic studies performed on the NC group as an infrared probe, when it is bonded to an indole ring. Here, we systematically study the NC stretching mode of two model compounds, 5-isocyano-1H-indole (5ICI) and 5-isocyano-1-methyl-1H-indole (NM5ICI), using Fourier transform infrared (FTIR) spectroscopy. The NC stretching frequency is shown to be strongly dependent on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when NC is bonded to an indole ring. Infrared pump–probe studies of 5ICI in DMSO and in EtOH further support that the NC stretching mode could be used as a site-specific infrared probe for local environments when NC is bonded to an indole ring.

Probe of Alcohol Structures in the Gas and Liquid States Using C⁻H Stretching Raman Spectroscopy

Vibrational spectroscopy is a powerful tool for probing molecular structures and dynamics since it offers a unique fingerprint that allows molecular identification. One of important aspects of applying vibrational spectroscopy is to develop the probes that can characterize the related properties of molecules such as the conformation and intermolecular interaction. Many examples of vibrational probes have appeared in the literature, including the azide group (⁻N₃), amide group (⁻CONH₂), nitrile groups (⁻CN), hydroxyl group (⁻OH), ⁻CH group and so on. Among these probes, the ⁻CH group is an excellent one since it is ubiquitous in organic and biological molecules and the C⁻H stretching vibrational spectrum is extraordinarily sensitive to the local molecular environment. However, one challenge encountered in the application of C⁻H probes arises from the difficulty in the accurate assignment due to spectral congestion in the C⁻H stretching region. In this paper, recent advances in the complete assignment of C⁻H stretching spectra of aliphatic alcohols and the utility of C⁻H vibration as a probe of the conformation and weak intermolecular interaction are outlined. These results fully demonstrated the potential of the ⁻CH chemical group as a molecular probe.