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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
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.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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You M, Gao Z, Zhou L, Guo C, Guo Q. Investigation of the Vibrational Characteristics of 6-Isocyano-1-Methyl-1H-Indole: Utilizing the Isonitrile Group as an Infrared Probe. Molecules 2023; 28:6939. [PMID: 37836782 PMCID: PMC10574170 DOI: 10.3390/molecules28196939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
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.
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Affiliation(s)
- Min You
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Zilin Gao
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China;
| | - Changyuan Guo
- Key Laboratory of Intelligent Air-Ground Cooperative Control for Universities in Chongqing, College of Automation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Qiang Guo
- Shanxi Province Key Laboratory of Higee-Oriented Chemical Engineering, School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
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Hong J, Zhou DX, Hao HX, Zhao M, Bian HT. Ultrafast infrared spectroscopic study of microscopic structural dynamics in pH stimulus-responsive hydrogels. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jian Hong
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - De-xia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Hong-xing Hao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Min Zhao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Hong-tao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
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Djordjevic I, Wicaksono G, Solic I, Steele TW. Diazoalkane decay kinetics from UVA-active protein labelling molecules: Trifluoromethyl phenyl diazirines. RESULTS IN CHEMISTRY 2020. [DOI: 10.1016/j.rechem.2020.100066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Zhan Y, Zeng Y, Li L, Luo F, Qiu B, Lin Z, Guo L. Ratiometric Fluorescent Hydrogel Test Kit for On-Spot Visual Detection of Nitrite. ACS Sens 2019; 4:1252-1260. [PMID: 30900872 DOI: 10.1021/acssensors.9b00125] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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.
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Affiliation(s)
- Yuanjin Zhan
- Institute of Nanomedicine and Nanobiosensing, MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Yanbo Zeng
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Lei Li
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Fang Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Bin Qiu
- Institute of Nanomedicine and Nanobiosensing, MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Zhenyu Lin
- Institute of Nanomedicine and Nanobiosensing, MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Longhua Guo
- Institute of Nanomedicine and Nanobiosensing, MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
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You M, Zhou L, Huang X, Wang Y, Zhang W. Isonitrile-Derivatized Indole as an Infrared Probe for Hydrogen-Bonding Environments. Molecules 2019; 24:molecules24071379. [PMID: 30965674 PMCID: PMC6480494 DOI: 10.3390/molecules24071379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/24/2019] [Accepted: 03/30/2019] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Xinyue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Yang Wang
- Department of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
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Wei Q, Zhou D, Li X, Chen Y, Bian H. Structural Dynamics of Dimethyl Sulfoxide Aqueous Solutions Investigated by Ultrafast Infrared Spectroscopy: Using Thiocyanate Anion as a Local Vibrational Probe. J Phys Chem B 2018; 122:12131-12138. [DOI: 10.1021/acs.jpcb.8b10058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qianshun Wei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Xiaoqian Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Yuwan Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
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Huang XY, You M, Ran GL, Fan HR, Zhang WK. Ester-Derivatized indoles as fluorescent and infrared probes for hydration environments. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1805118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-yue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Guang-liu Ran
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Hao-ran Fan
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wen-kai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
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Yu Y, Fan W, Wang Y, Zhou X, Sun J, Liu S. Probe of Alcohol Structures in the Gas and Liquid States Using C⁻H Stretching Raman Spectroscopy. SENSORS (BASEL, SWITZERLAND) 2018; 18:E2061. [PMID: 29958405 PMCID: PMC6068699 DOI: 10.3390/s18072061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 01/16/2023]
Abstract
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.
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Affiliation(s)
- Yuanqin Yu
- Department of Physics, Anhui University, Hefei 230601, China.
| | - Wei Fan
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Yuxi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Jin Sun
- Department of Physics, Anhui University, Hefei 230601, China.
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
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