1
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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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2
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Chen CG, Amadei A, D'Abramo M. Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124096. [PMID: 38442616 DOI: 10.1016/j.saa.2024.124096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
In a recent paper, we proposed a scheme to describe the relaxation mechanism of the excited Indole in aqueous solution, involving the fluctuations among the diabatic electronic states 1Lb, 1La and 1πσ∗. Such a theoretical and computational model reproduced accurately the available experimental data at room temperature. Following these results, in the present work, we model the complex temperature dependence of the fluorescence properties of Indole in aqueous solution, with results further validating the proposed relaxation scheme. This scheme is able to explain the temperature effects on the fluorescence behavior indicating the water fluctuations as the main cause of (i) the stabilization of the dark state (1πσ∗) and (ii) the increase in temperature of the kinetics of the irreversible transition towards such a state.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, Rome, 00185, Italy
| | - Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Via della Ricerca Scientifica, 1, Rome, 00133, Italy.
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, Rome, 00185, Italy.
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3
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Abou-Hatab S, Matsika S. Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes. Phys Chem Chem Phys 2024; 26:4511-4523. [PMID: 38240574 DOI: 10.1039/d3cp04844f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.
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4
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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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5
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Yang Y, Liu J, Feng RR, Zhang W, Gai F. C≡N Stretching Frequency as a Convenient Reporter of Charge Separation in Molecular Systems. J Phys Chem B 2023; 127:6999-7003. [PMID: 37525395 DOI: 10.1021/acs.jpcb.3c02707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Previously, several studies have shown that, for a set of structurally related nitrile compounds, there could be a linear relationship between the total charge on the nitrile group (qCN) and its stretching frequency (νCN). However, it is unclear whether the corresponding frequency and charge properties of structurally different nitrile compounds can be described by a single linear νCN-qCN relationship. Herein, we compute the qCN magnitudes of a large number of nitrile-containing molecules whose νCN values cover a spectral range of ca. 200 cm-1 and are measured under different experimental conditions. Our results reveal that νCN indeed exhibits a linear dependence on qCN, with a slope of 637 ± 30 cm-1/charge. Because the nitrile moiety is a commonly used building block in electronic donor-acceptor (D-A) molecular systems, we believe that this linear relationship will find utility in a wide range of applications where such D-A constructs are used, such as in organic photovoltaic assemblies. In addition, we apply this linear relationship to characterize the degree of charge transfer upon photoexcitation of two indole derivatives, 5-cyanoindole and 6-cyanoindole, and are able to show that in both cases, the fluorescence emission arises from a charge-transfer or La state.
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Affiliation(s)
- Yuyao Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingsong Liu
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- 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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6
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Chen CG, Giustini M, D'Abramo M, Amadei A. Unveiling the Excited State Dynamics of Indole in Solution. J Chem Theory Comput 2023. [PMID: 37329333 DOI: 10.1021/acs.jctc.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In this paper, we reconstruct in detail the dynamics of the emitting electronic excited state of aqueous indole, investigating its relaxation mechanism and kinetics to be related to the time-dependent fluorescence signal. Taking advantage of the results shown in a very recent paper, we were able to model the relaxation process in solution in terms of the transitions between two gas-phase singlet electronic states (1La and 1Lb), subsequently irreversibly relaxing to the gas-phase singlet dark state (1πσ*). A comparison of the results with the available experimental data shows that the relaxation mechanism we obtain by our theoretical-computational model is reliable, reproducing rather accurately all the experimental observables.
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Affiliation(s)
| | - Mauro Giustini
- Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
| | - Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Rome 00133, Italy
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7
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Yuan Y, Liu J, Feng RR, Zhang W, Gai F. Photophysics of Two Indole-Based Cyan Fluorophores. J Phys Chem B 2023; 127:4508-4513. [PMID: 37171997 DOI: 10.1021/acs.jpcb.3c01739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
For the purpose of searching for new biological fluorophore, we assess the photophysical properties of two indole derivatives, 4-cyano-7-azaindole (4CN7AI) and 1-methyl-4-cyano-7-azaindole (1M4CN7AI), in a series of solvents. We find that (1) the absorption spectra of both derivatives are insensitive to solvents and are red-shifted from that of indole, having a maximum absorption wavelength of ca. 318 nm and a broad profile that extends beyond 370 nm; (2) both derivatives emit in the blue to green spectral range with a large Stokes shift, for example, in H2O, the maximum emission wavelength of 4CN7AI (1M4CN7AI) is at ca. 455 nm (470 nm); (3) 4CN7AI has a higher fluorescence quantum yield (QY) and a longer fluorescence lifetime (τF) in aprotic solvents than in protic solvents, for example, QY (τF) = 0.72 ± 0.04 (7.6 ± 0.8 ns) in tetrahydrofuran and QY (τF) = 0.29 ± 0.03 (6.2 ± 0.6 ns) in H2O; (4) in all of the solvents used except H2O, the fluorescence QY (τF) of 1M4CN7AI is equal to or higher (longer) than 0.69 ± 0.03 (11.2 ± 0.7 ns). Taken together, these results suggest that the corresponding non-natural amino acids, 4-cyano-7-azatryptophan and 1-methyl-4-cyano-7-azatryptophan, could be useful as biological fluorophores.
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Affiliation(s)
- Yu Yuan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingsong Liu
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- 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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8
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Yang Y, Feng RR, Gai F. 4-Cyanotryptophan as a Sensitive Fluorescence Probe of Local Electric Field of Proteins. J Phys Chem B 2023; 127:514-519. [PMID: 36598839 DOI: 10.1021/acs.jpcb.2c07605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Electrostatic interactions are key determinants of protein structure, dynamics, and function. Since protein electrostatics are nonuniform, assessment of the internal electric fields (EFs) of proteins requires spatial resolution at the amino acid residue level. In this regard, vibrational Stark spectroscopy, in conjunction with various unnatural amino acid-based vibrational probes, has become a common method for site-specific interrogation of protein EFs. However, application of this method is often limited to proteins with relatively high solubility, due to the intrinsically low oscillator strength of vibrational transitions. Therefore, it would be useful to develop an alternative method that can overcome this limitation. To this end, we show that, using solvatochromic study and molecular dynamics simulations, the frequency of maximum emission intensity of the fluorophore of 4-cyanotryptophan (4CN-Trp), 3-methyl-1H-indole-4-carbonitrile, exhibits a linear dependence on the local EF. Since the absorption and emission spectra of 4CN-Trp are easily distinguishable from those of naturally occurring aromatic amino acids, we believe that this linear relationship provides an easier and more sensitive means to determine the local EF of proteins.
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Affiliation(s)
- Yuyao Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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9
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Morshedi M, Nolden O, Janke P, Haselbach W, Schmitt M, Gilch P. The photophysics of 2-cyanoindole probed by femtosecond spectroscopy. Photochem Photobiol Sci 2022; 22:745-759. [PMID: 36495408 DOI: 10.1007/s43630-022-00348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
AbstractThe photophysics of 2-cyanoindole (2-CI) in solution (water, 2,2,2-trifluoroethanol, acetonitrile‚ and tetrahydrofuran) was investigated by steady-state as well as time resolved fluorescence and absorption spectroscopy. The fluorescence quantum yield of 2-cyanoindole is strongly sensitive to the solvent. In water the quantum yield is as low as 4.4 × 10–4. In tetrahydrofuran, it amounts to a yield of 0.057. For 2-CI dissolved in water, a bi-exponential fluorescence decay with time constants of ∼1 ps and ∼8 ps is observed. For short wavelength excitation (266 nm) the initial fluorescence anisotropy is close to zero. For excitation with 310 nm it amounts to 0.2. In water, femtosecond transient absorption reveals that the fluorescence decay is solely due to internal conversion to the ground state. In aprotic solvents, the fluorescence decay takes much longer (acetonitrile: ∼900 ps, tetrahydrofuran: ∼2.6 ns) and intersystem crossing contributes.
Graphical abstract
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10
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A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238135. [PMID: 36500228 PMCID: PMC9739849 DOI: 10.3390/molecules27238135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
Abstract
In this paper, we introduce specific approximations to simplify the vibronic treatment in modeling absorption and emission spectra, allowing us to include a huge number of vibronic transitions in the calculations. Implementation of such a simplified vibronic treatment within our general approach for modelling vibronic spectra, based on molecular dynamics simulations and the perturbed matrix method, provided a quantitative reproduction of the absorption and emission spectra of aqueous indole with higher accuracy than the one obtained when using the existing vibronic treatment. Such results, showing the reliability of the approximations employed, indicate that the proposed method can be a very efficient and accurate tool for computational spectroscopy.
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11
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Liu J, Feng RR, Zhou L, Gai F, Zhang W. Photoenhancement of the C≡N Stretching Vibration Intensity of Aromatic Nitriles. J Phys Chem Lett 2022; 13:9745-9751. [PMID: 36222647 DOI: 10.1021/acs.jpclett.2c02418] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The C≡N stretching vibration is a versatile infrared (IR) reporter that is useful for a wide range of applications. Aiming to further expand its spectroscopic utility, herein, we show that, using 4-cyanoindole and 4-cyano-7-azaindole as examples, photoexcitation can significantly shift the frequency (νCN) and enhance the molar extinction coefficient (εCN) of this vibrational mode of aromatic nitriles and that, for these indole derivatives, the enhancement factor can reach 13. Moreover, we find that while solvent relaxation at the excited electronic state(s) always leads to an increase in εCN, its effect on νCN depends on the solute and the solvent. Taken together, these results demonstrate that solvent relaxation can differently affect the local environment of the nitrile group and its conjugation with the indole ring and, more importantly, that the C≡N stretching vibration can serve as a sensitive IR probe of charge and electron transfer processes in which an aromatic nitrile is involved.
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Affiliation(s)
- Jingsong Liu
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Liang Zhou
- 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
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
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12
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Micikas RJ, Acharyya A, Smith AB, Gai F. Synthesis and characterization of the fluorescence utility of two Visible-Light-Absorbing tryptophan derivatives. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Min A, Kim J, Moon CJ, Ahn A, Park J, Choi MY. Spectroscopic and theoretical studies of jet‐cooled 3‐cyanoindole ammonia clusters in the gas phase. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ahreum Min
- Core‐Facility Center for Photochemistry & Nanomaterials Gyeongsang National University Jinju Republic of Korea
| | - Jiwon Kim
- Department of Chemistry (BK21 FOUR), Research Institute of Natural Sciences Gyeongsang National University Jinju Republic of Korea
| | - Cheol Joo Moon
- Department of Chemistry (BK21 FOUR), Research Institute of Natural Sciences Gyeongsang National University Jinju Republic of Korea
| | - Ahreum Ahn
- Center for Supercomputing Applications Korea Institute of Science and Technology Information Daejeon Republic of Korea
| | - Juhyeon Park
- Department of Chemistry (BK21 FOUR), Research Institute of Natural Sciences Gyeongsang National University Jinju Republic of Korea
| | - Myong Yong Choi
- Core‐Facility Center for Photochemistry & Nanomaterials Gyeongsang National University Jinju Republic of Korea
- Department of Chemistry (BK21 FOUR), Research Institute of Natural Sciences Gyeongsang National University Jinju Republic of Korea
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14
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Mukherjee D, Ahmed IA, Gai F. Site-Specific Interrogation of Protein Structure and Stability. Methods Mol Biol 2022; 2376:65-87. [PMID: 34845603 DOI: 10.1007/978-1-0716-1716-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To execute their function or activity, proteins need to possess variability in local electrostatic environment, solvent accessibility, structure, and stability. However, assessing any protein property in a site-specific manner is not easy since native spectroscopic signals often lack the needed specificity. One strategy that overcomes this limitation is to use unnatural amino acids that exhibit distinct spectroscopic features. In this chapter, we describe several such unnatural amino acids (UAAs) and their respective applications in site-specific interrogation of protein structure and stability using standard biophysical methods, including circular dichroism (CD), infrared (IR), and fluorescence spectroscopies.
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Affiliation(s)
| | - Ismail A Ahmed
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Henrichs C, Zimmermann S, Hebestreit ML, Schmitt M. Excited state structure of isolated 2-cyanoindole and the binary 2-cyanoindole-(H2O)1 cluster from a combined Franck-Condon and rotational constants fit. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Acharyya A, Zhang W, Gai F. Tryptophan as a Template for Development of Visible Fluorescent Amino Acids. J Phys Chem B 2021; 125:5458-5465. [PMID: 34029101 DOI: 10.1021/acs.jpcb.1c02321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most biological systems, at both molecular and cellular levels, are intrinsically complex, diverse, and nonfluorescent. Therefore, studying their structures, dynamics, and interactions via fluorescence-based methods requires incorporation of one or multiple external fluorophores that would not significantly affect any native property of the system in question. This requirement necessitates the development of a diverse set of fluorescence reporters that differ in chemical, physical, and photophysical properties. Herein, we offer our perspective on the need for, recent progress in, and future directions of developing tryptophan-based fluorescent amino acids.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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17
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Hebestreit ML, Lartian H, Henrichs C, Kühnemuth R, Meerts WL, Schmitt M. Excited state dipole moments and lifetimes of 2-cyanoindole from rotationally resolved electronic Stark spectroscopy. Phys Chem Chem Phys 2021; 23:10196-10204. [PMID: 33951126 DOI: 10.1039/d1cp00097g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The permanent dipole moments of 2-cyanoindole (cyanoindole = CNI) in its ground and lowest excited singlet states have been determined from rotationally resolved electronic Stark spectroscopy under jet-cooled conditions. From the orientation of the transition dipole moment and the geometry changes upon electronic excitation the lowest excited singlet state could be shown to be of Lb-symmetry. The general statement, that the La-state has the larger permanent dipole moment of the two lowest excited singlet states, will be challenged in this contribution. On the basis of the different electronic nature of the first excited singlet state the behavior of 2-, 3-, 4- and 5-CNI is discussed. The excited state lifetime of isolated 2-CNI in the gas phase has been determined to be 9.4 ns. This value is compared to the excited state lifetime in ethyl acetate solution of 2.6 ns, which was quantified with a Strickler-Berg analysis. Using water as solvent shortens the 2-CNI lifetime to <40 ps. The reason for this drastic shortening is discussed in detail. Additionally, the rotationally resolved electronic spectrum of 2-CNI(1-d1) has been measured and analyzed.
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Affiliation(s)
- Marie-Luise Hebestreit
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
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18
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Micikas RJ, Ahmed IA, Acharyya A, Smith AB, Gai F. Tuning the electronic transition energy of indole via substitution: application to identify tryptophan-based chromophores that absorb and emit visible light. Phys Chem Chem Phys 2021; 23:6433-6437. [PMID: 33710175 DOI: 10.1039/d0cp06710e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fluorescent amino acids (FAAs) offer significant advantages over fluorescent proteins in applications where the fluorophore size needs to be limited or minimized. A long-sought goal in biological spectroscopy/microcopy is to develop visible FAAs by modifying the indole ring of tryptophan. Herein, we examine the absorption spectra of a library of 4-substituted indoles and find that the frequency of the absorption maximum correlates linearly with the global electrophilicity index of the substituent. This finding permits us to identify two promising candidates, 4-formyltryptophan (4CHO-Trp) and 4-nitrotryptophan (4NO2-Trp), both of which can be excited by visible light. Further fluorescence measurements indicate that while 4CHO-indole (and 4CHO-Trp) emits cyan fluorescence with a reasonably large quantum yield (ca. 0.22 in ethanol), 4NO2-indole is essentially non-fluorescent, suggesting that 4CHO-Trp (4NO2-Trp) could be useful as a fluorescence reporter (quencher). In addition, we present a simple method for synthesizing 4CHO-Trp.
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Affiliation(s)
- Robert J Micikas
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
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19
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Abou-Hatab S, Carnevale V, Matsika S. Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution. J Chem Phys 2021; 154:064104. [PMID: 33588532 PMCID: PMC7878019 DOI: 10.1063/5.0038342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/20/2021] [Indexed: 11/14/2022] Open
Abstract
Modeling the optical spectra of molecules in solution presents a challenge, so it is important to understand which of the solvation effects (i.e., electrostatics, mutual polarization, and hydrogen bonding interactions between solute and solvent molecules) are crucial in reproducing the various features of the absorption and fluorescence spectra and to identify a sufficient theoretical model that accurately captures these effects with minimal computational cost. In this study, we use various implicit and explicit solvation models, such as molecular dynamics coupled with non-polarizable and polarizable force fields, as well as Car-Parrinello molecular dynamics, to model the absorption and fluorescence spectra of indole in aqueous solution. The excited states are computed using the equation of motion coupled cluster with single and double excitations combined with the effective fragment potential to represent water molecules, which we found to be a computationally efficient approach for modeling large solute-solvent clusters at a high level of quantum theory. We find that modeling mutual polarization, compared to other solvation effects, is a dominating factor for accurately reproducing the position of the peaks and spectral line shape of the absorption spectrum of indole in solution. We present an in-depth analysis of the influence that different solvation models have on the electronic excited states responsible for the features of the absorption spectra. Modeling fluorescence is more challenging since it is hard to reproduce even the correct emitting state, and force field parameters need to be re-evaluated.
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Affiliation(s)
- Salsabil Abou-Hatab
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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20
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Excited state structure of isolated 4-cyanoindole from a combined Franck-Condon and rotational constants analysis†. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Laxman K, Reddy BPK, Mishra SK, Gopal MB, Robinson A, De A, Srivastava R, Ravikanth M. BF 2-Oxasmaragdyrin Nanoparticles: A Non-toxic, Photostable, Enhanced Non-radiative Decay-Assisted Efficient Photothermal Cancer Theragnostic Agent. ACS APPLIED MATERIALS & INTERFACES 2020; 12:52329-52342. [PMID: 33170618 DOI: 10.1021/acsami.0c13326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photothermal therapy (PTT), a simple and minimally invasive procedure, is an attractive option for cancer therapy. To date, inorganic agents have been widely employed as photothermal agents; however, organic molecules may provide a solution to rapid metabolic/in vivo clearance. Herein, we prepared lipid (S 75)-stabilized meso-tritolyl-BF2-oxasmaragdyrin nanoparticles (TBSNPs) using thin-film hydration and homogenization. Assessment of the physicochemical properties of the TBSNPs reveals the formation of particles of size <12 nm stabilized within the lipid matrix. The TBSNPs exhibit near infrared fluorescence (NIRF) being accompanied by an increase in non-radiative decay, leading to excellent photothermal properties. In vitro studies demonstrate excellent biocompatibility, hemocompatibility, cellular internalization, and photothermal efficacy (p = 0.0004). Extensive in vivo assessment of TBSNPs also highlights the non-toxic nature of the material and passive tumor homing. The strong NIRF exhibited by the material is exploited for whole-body imaging in the rodent model. The novel material also shows excellent photothermal efficacy (p = 0.0002) in a 4T1 xenograft mice model. The organic nature of the material coupled with its small size and strong NIRF provides an advantage for bio-elimination and potential clinical image-guided therapy over the inorganic counterparts.
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Affiliation(s)
- Kandala Laxman
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- School of Chemistry, Monash University, (Building 23, Room 114C), Wellington Road Clayton, Melbourne, Victoria 3800, Australia
| | - B Pradeep K Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sumit K Mishra
- Molecular Functional Imaging Laboratory, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
- Department of Life Sciences, Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Maddala Bala Gopal
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Andrea Robinson
- School of Chemistry, Monash University, (Building 23, Room 114C), Wellington Road Clayton, Melbourne, Victoria 3800, Australia
| | - Abhijit De
- Molecular Functional Imaging Laboratory, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
- Department of Life Sciences, Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Rohit Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Fluorine induced conformational switching and modulation in photophysical properties of 7-fluorotryptophan: Spectroscopic, quantum chemical calculation and molecular dynamics simulation studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2020. [DOI: 10.1016/j.jpap.2020.100011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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23
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Abstract
Most biological molecules are intrinsically non- or weakly-fluorescent, hence requiring labeling with an external fluorophore(s) to be studied via fluorescence-based techniques. However, such labeling could perturb the native property of the system in question. One effective strategy to minimize such undesirable perturbation is to use fluorophores that are simple analogs of natural amino acids. In this chapter, we describe the synthesis and spectroscopic utility of two indole-based fluorophores, 4-cynaotryprophan (4CN-Trp) and 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), with a focus on 4CN-Trp. This unnatural amino acid, which is only slightly larger than its natural counterpart, tryptophan (Trp), exhibits unique photophysical properties, making it a versatile fluorophore in biological spectroscopic and imaging applications. Through several specific examples, we highlight its broad utility in the study of various biological problems and processes.
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24
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Acharyya A, Shin D, Troxler T, Gai F. Can glycine betaine denature proteins? Phys Chem Chem Phys 2020; 22:7794-7802. [PMID: 32242578 DOI: 10.1039/d0cp00397b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation-π interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two β-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such non-monotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB's stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation-π binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation-π interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Dayoung Shin
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Thomas Troxler
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
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25
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You M, Fan H, Wang Y, Zhang W. Aldehyde-derivatized indoles as fluorescent probes for hydration environments. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Abou-Hatab S, Matsika S. Theoretical Investigation of Positional Substitution and Solvent Effects on n-Cyanoindole Fluorescent Probes. J Phys Chem B 2019; 123:7424-7435. [DOI: 10.1021/acs.jpcb.9b05961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Salsabil Abou-Hatab
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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27
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Ahmed IA, Rodgers JM, Eng C, Troxler T, Gai F. PET and FRET utility of an amino acid pair: tryptophan and 4-cyanotryptophan. Phys Chem Chem Phys 2019; 21:12843-12849. [PMID: 31179453 PMCID: PMC6587589 DOI: 10.1039/c9cp02126d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methods based on fluorescence resonance energy transfer (FRET) and photo-induced electron transfer (PET) are widely used in the biological sciences, employing mostly dye-based FRET and PET pairs. While very useful and important, dye-based reporters are not always applicable without concern, for example, in cases where the fluorophore size needs to be minimized. Therefore, development and characterization of smaller, ideally amino acid-based PET and FRET pairs will expand the biological spectroscopy toolbox to enable new applications. Herein, we show that, depending on the excitation wavelength, tryptophan and 4-cyanotrptophan can interact with each other via the mechanism of either energy or electron transfer, hence constituting a dual FRET and PET pair. The biological utility of this amino acid pair is further demonstrated by applying it to study the end-to-end collision rate of a short peptide, the mode of interaction between a ligand and BSA, and the activity of a protease.
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Affiliation(s)
- Ismail A. Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey M. Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christina Eng
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Thomas Troxler
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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28
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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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29
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Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. 4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules 2019; 24:E602. [PMID: 30744004 PMCID: PMC6384856 DOI: 10.3390/molecules24030602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 11/16/2022] Open
Abstract
Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA⁻protein interactions.
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Affiliation(s)
- Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Christina M Eng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jeffrey M Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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30
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Hebestreit ML, Schneider M, Lartian H, Betz V, Heinrich M, Lindic M, Choi MY, Schmitt M. Structures, dipole moments and excited state lifetime of isolated 4-cyanoindole in its ground and lowest electronically excited singlet states. Phys Chem Chem Phys 2019; 21:14766-14774. [PMID: 31222195 DOI: 10.1039/c9cp01618j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rotationally resolved electronic spectrum of 4-cyanoindole and some N-D and C-D deuterated isotopologues has been measured and analyzed. Dipole moments in the ground and electronically excited state have been determined, using electronic Stark spectroscopy. From the geometry changes upon excitation, orientation of the transition dipole moment, and the values for the permanent dipole moments, the lowest excited singlet state could be shown to be of La symmetry. The excited state lifetime of isolated 4-cyanoindole has been determined to be 11 ns, while for the ringdeuterated isotopologues lifetimes between 5 and 6 ns have been found. The different behavior of 3-, 4-, and 5-cyanoindole is discussed on the basis of the different electronic nature of the electronically excited singlet states.
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Affiliation(s)
- Marie-Luise Hebestreit
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Michael Schneider
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Hilda Lartian
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Vivienne Betz
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Michael Heinrich
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Mirko Lindic
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Myong Yong Choi
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Michael Schmitt
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
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31
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Synthesis, Crystal Structure, DFT Studies, Docking Studies, and Fluorescent Properties of 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile. CRYSTALS 2018. [DOI: 10.3390/cryst9010024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile (1) has been identified as a neurobiological fluorescent ligand that may be used to develop receptor and enzyme binding affinity assays. Compound 1 was synthesized using an optimized microwave irradiation reaction, and crystallized from ethanol. Crystallization occurred in the orthorhombic space group P212121 with unit cell parameters: a = 6.4487(12) Å, b = 13.648(3) Å, c = 16.571(3) Å, V = 1458(5) Å3, Z = 4. Density functional theory (DFT) (B3LYP/6-311++G (d,p)) calculations of 1 were carried out. Results indicated that the optimized geometry was similar to the experimental results, with a root-mean-squared deviation of 0.143 Å. In this paper, frontier molecular orbital energies and net atomic charges are discussed with a focus on potential biological interactions. Docking experiments within the active site of the neuronal nitric oxide synthase (nNOS) protein crystal structure were carried out and analyzed. Important binding interactions between the DFT-optimized structure and amino acids within the nNOS active site were identified that explained the strong NOS binding affinity reported. Fluorescent properties of 1 were studied using aprotic solvents of different polarities. Compound 1 showed the highest fluorescence intensity in polar solvents, with excitation and emission maximum values of 336 nm and 380 nm, respectively.
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Mishra J, Mishra AK. Effect of Indole-3-Carbinol on Dimyristoylphosphatidylcholine Multilamellar Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11886-11897. [PMID: 30189729 DOI: 10.1021/acs.langmuir.8b02769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study reports the interaction of indole-3-carbinol (I3C), which is a chemopreventive reagent, with an artificial model membrane {(dimyristoylphosphatidylcholine (DMPC) multilamellar vesicles (MLVs)}, using the intrinsic fluorescence properties of I3C, extrinsic fluorescence properties of Nile Red (NR), differential scanning calorimetry (DSC), dynamic light scattering (DLS), and confocal microscopy. The intrinsic fluorescence of I3C helps to provide information about its location, partitioning ability, and sensitivity toward the phase-transition temperature of liposomes, confirmed by cetylpyridinium chloride (CPC) quenching study, partition coefficient values {(4.60 ± 0.1) × 105 (solid gel phase) and (7.29 ± 0.1) × 105 M-1 (liquid crystalline phase)} and temperature-dependent emission behavior of I3C. I3C perturbs the DMPC MLVs above 15 mol %, as observed using the fluorescence properties of NR, DSC, and DLS data. This perturbation occurs as a consequence of interfacial hydration of the DMPC MLVs, which was clearly indicated by the fluorescence properties (emission intensity, fluorescence lifetime, and nonextensive distribution analysis) of NR.
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Affiliation(s)
- Jhili Mishra
- Department of Chemistry , Indian Institute of Technology Madras , Chennai 600 036 , India
| | - Ashok Kumar Mishra
- Department of Chemistry , Indian Institute of Technology Madras , Chennai 600 036 , India
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33
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Schneider M, Hebestreit ML, Lindic MM, Parsian H, Torres-Boy AY, Álvarez-Valtierra L, Meerts WL, Kühnemuth R, Schmitt M. Rotationally resolved electronic spectroscopy of 3-cyanoindole and the 3-cyanoindole-water complex. Phys Chem Chem Phys 2018; 20:23441-23452. [PMID: 30182125 DOI: 10.1039/c8cp04020f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rotationally resolved electronic spectra of the origin bands of 3-cyanoindole, 3-cyanoindole(d1), and the 3-cyanoindole-(H2O)1 cluster have been measured and analyzed using evolutionary algorithms. For the monomer, permanent dipole moments of 5.90 D for the ground state, and of 5.35 D for the lowest excited singlet state have been obtained from electronic Stark spectroscopy. The orientation of the transition dipole moment is that of an 1Lb state for the monomer. The water moiety in the water cluster could be determined to be trans-linearly bound to the NH group of 3-cyanoindole, with an NHO hydrogen bond length of 201.9 pm in the electronic ground state. Like the 3-cyanoindole monomer, the 3-cyanoindole-water cluster also shows an 1Lb-like excited singlet state. The excited state lifetime of isolate 3-cyanoindole in the gas phase has been determined to be 9.8 ns, and that of 3-cyanoindole(d1) has been found to be 14.8 ns, while that of the 1 : 1 water cluster is considerably shorter (3.6 ns). The excited state lifetime of 3-cyanoindole(d1) in D2O solution has been found to be smaller than 20 ps.
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Affiliation(s)
- Michael Schneider
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Marie-Luise Hebestreit
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Mirko Matthias Lindic
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - Hilda Parsian
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
| | - América Yareth Torres-Boy
- División de Ciencias e Ingenierías, Universidad de Guanajuato-Campus León, León, Guanajuato 37150, Mexico
| | - Leonardo Álvarez-Valtierra
- División de Ciencias e Ingenierías, Universidad de Guanajuato-Campus León, León, Guanajuato 37150, Mexico
| | - W Leo Meerts
- Radboud University, Institute for Molecules and Materials, Felix Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Ralf Kühnemuth
- Heinrich-Heine-Universität, Lehrstuhl für Molekulare Physikalische Chemie, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany.
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34
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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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35
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Passow KT, Harki DA. 4-Cyanoindole-2'-deoxyribonucleoside (4CIN): A Universal Fluorescent Nucleoside Analogue. Org Lett 2018; 20:4310-4313. [PMID: 29989830 PMCID: PMC6168291 DOI: 10.1021/acs.orglett.8b01746] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The synthesis and characterization of a universal and fluorescent nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CIN), and its incorporation into DNA is described. 4CIN is a highly efficient fluorophore with quantum yields >0.90 in water. When incorporated into duplex DNA, 4CIN pairs equivalently with native nucleobases and has uniquely high quantum yields ranging from 0.15 to 0.31 depending on sequence and hybridization contexts, surpassing that of 2-aminopurine, the prototypical nucleoside fluorophore. 4CIN constitutes a new isomorphic nucleoside for diverse applications.
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Affiliation(s)
- Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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36
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Mukherjee D, Ortiz Rodriguez LI, Hilaire MR, Troxler T, Gai F. 7-Cyanoindole fluorescence as a local hydration reporter: application to probe the microheterogeneity of nine water-organic binary mixtures. Phys Chem Chem Phys 2018; 20:2527-2535. [PMID: 29313858 DOI: 10.1039/c7cp07160d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Considerable efforts have been devoted to the development of spectroscopic probes that are sensitive to water and can be used to monitor, for example, biological and chemical processes involving dehydration or hydration. Continuing this line of research, herein we show that 7-cyanoindole can serve as a sensitive fluorescence probe of hydration as its fluorescence properties, including intensity, peak wavelength and lifetime, depend on the amount of water in nine water-organic solvent mixtures. Our results indicate that 7-cyanoindole is not only able to reveal the underlying microheterogeneity of these binary solvent systems, but also offers distinct advantages. These include: (1) its fluorescence intensity increases more than ten times upon going from a hydrated to a dehydrated environment; (2) its peak wavelength shifts as much as 35 nm upon dehydration; (3) its single-exponential fluorescence decay lifetime increases from 2.0 ns in water to 8-16 ns in water-organic binary mixtures, making it viable to distinguish between differently hydrated environments via fluorescence lifetime measurements; and (4) its absorption spectrum is significantly red-shifted from that of indole, making selective excitation of its fluorescence possible in the presence of naturally occurring amino-acid fluorophores. Moreover, we find that for seven binary mixtures the fluorescence lifetimes of 7-cyanoindole measured at solvent compositions where maximum microheterogeneity occurs correlate linearly with the peak wavenumbers of its fluorescence spectra obtained in the respective pure organic solvents. This suggests that the microheterogeneities of these binary mixtures bear certain similarity, a phenomenon that warrants further investigation.
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Affiliation(s)
- Debopreeti Mukherjee
- Department of Chemistry University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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van Wilderen LJGW, Brunst H, Gustmann H, Wachtveitl J, Broos J, Bredenbeck J. Cyano-tryptophans as dual infrared and fluorescence spectroscopic labels to assess structural dynamics in proteins. Phys Chem Chem Phys 2018; 20:19906-19915. [DOI: 10.1039/c8cp00846a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
By moving the cyano group position on the indole ring, both artificial amino acids report differently to their microscopic environment.
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Affiliation(s)
| | - H. Brunst
- Institute of Biophysics
- Johann-Wolfgang-Goethe Universität
- Frankfurt am Main
- Germany
| | - H. Gustmann
- Institute of Physical and Theoretical Chemistry
- Johann-Wolfgang-Goethe Universität
- Frankfurt am Main
- Germany
| | - J. Wachtveitl
- Institute of Physical and Theoretical Chemistry
- Johann-Wolfgang-Goethe Universität
- Frankfurt am Main
- Germany
| | - J. Broos
- Laboratory of Biophysical Chemistry and GBB (Groningen Biomolecular Science and Biotechnology Institute)
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - J. Bredenbeck
- Institute of Biophysics
- Johann-Wolfgang-Goethe Universität
- Frankfurt am Main
- Germany
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