1
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Nasr MS, Talaat W, Morshedy S, Kaddah MMY, Omran G, Keshk RM. A new fluorescence probe for sofosbuvir analysis in dosage form and spiked human plasma. LUMINESCENCE 2024; 39:e4742. [PMID: 38637644 DOI: 10.1002/bio.4742] [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] [Received: 07/17/2023] [Revised: 03/09/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
A simple, rapid, and low-cost technique was developed to allow reliable analysis of the anti-hepatitis C drug sofosbuvir in bulk, tablet form, and spiked human plasma. This method depends on the ability of sofosbuvir to quench the fluorescence of the newly synthesized 2-amino-3-cyano-4,6-dimethylpyridine (reagent 3). Elemental analysis and spectral data were used to validate the structure of the synthesized reagent. The newly synthesized reagent exhibited a satisfactory level of fluorescence emission at 365 nm after excitation at 247 nm. All experimental variables that might affect the quenching process were analyzed and optimized. Linearity, range, accuracy, precision, limit of detection (LOD), and limit of quantitation (LOQ) were all validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) guidelines. The concentration range was shown to be linear between 0.1 and 1.5 μg/mL. The technique was effectively utilized for sofosbuvir analysis in both its tablet dosage form and spiked human plasma, with mean percentage recoveries of 100.13 ± 0.35 and 94.26 ± 1.69, respectively.
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Affiliation(s)
- Mohamed S Nasr
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Wael Talaat
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Samir Morshedy
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Mohamed M Y Kaddah
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria, Egypt
| | - Gamal Omran
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Reda M Keshk
- Department of Chemistry, Faculty of Science, Damanhour University, Damanhour, Egypt
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2
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Russel NS, Kodali G, Stanley RJ, Narayanan M. Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study. J Phys Chem B 2023; 127:7858-7871. [PMID: 37698525 DOI: 10.1021/acs.jpcb.3c03618] [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: 09/13/2023]
Abstract
Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.
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Affiliation(s)
- Nadim Shahriar Russel
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- GlowDNA LLC., Malvern, Pennsylvania 19355, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Madhavan Narayanan
- Department of Physical Sciences, Benedictine University, 5700 College Rd, Lisle, Illinois 60532, United States
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3
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Zucolotto Cocca LH, Pelosi AG, Piguel S, Mendonça CR, Boni LD. Enhancement of optical properties of new purine nucleobases containing electron-donating and -withdrawing peripheral groups. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112524. [PMID: 35843082 DOI: 10.1016/j.jphotobiol.2022.112524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Nowadays, a great deal of attention has been focused on synthesizing highly fluorescent unnatural base analogs. This has been motivated by the need to overcome the lack of fluorescence of nucleic acids' natural bases. Fluorescent unnatural base analogs, such as purines, may be used in several applications, such as DNA or RNA optical spectroscopy studies. Moreover, for purines base analogs, the optical properties, for example, emission, can be tunable through molecular engineering, improving their applications as fluorescent probes. Looking in this direction, the synthesis and optical spectroscopic studies of a new set of purines base analogs are of foremost relevance. Here, an increase in the fluorescence quantum yield was observed in molecules with NH-π-CN arrangement. The two-photon absorption (2PA) cross-sections also increased for the lower energy 2PA state. The enhancement of both properties results in a two-photon brightness of 5 and 10 times higher than in compounds lacking the NH-π-CN arrangement. For the higher energy 2PA state, an excited state absorption contribution to the 2PA cross-section values was observed, that was verified through ultrafast transient absorption measurements. The higher 2PA brightness makes the purines base analogs promising candidates as fluorescent probes in RNA and DNA spectroscopic studies.
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Affiliation(s)
- Leandro H Zucolotto Cocca
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil.
| | - André G Pelosi
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil
| | - Sandrine Piguel
- Université Paris-Saclay, Faculté de Pharmacie, CNRS UMR 8076, 92296 Châtenay-Malabry, France
| | - Cleber Renato Mendonça
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil
| | - Leonardo De Boni
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil.
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4
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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5
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Zucolotto Cocca LH, Pelosi A, Sciuti LF, M. G. Abegão L, Kamada K, Piguel S, Renato Mendonça C, De Boni L. Two-photon brightness of highly fluorescent imidazopyridine derivatives: Two-photon and ultrafast transient absorption studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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7
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Zeng HH, Liu F, Hu LK, Deng J, Xie YP, Xiao W, Lai PQ, Wang Y, Feng YF, Yu JC. Fluorescence Turn-On Detection of Ascorbic Acid Using a Self-Assembled Lanthanide Polymer Nanoparticle. APPLIED SPECTROSCOPY 2020; 74:275-284. [PMID: 31617379 DOI: 10.1177/0003702819878155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ascorbic acid (AA), or vitamin C, is an important reactive biological molecule in vivo, and an abnormal level of AA is associated with many diseases. Therefore, the rapid, sensitive, and selective detection of AA levels is of significance in cases of medical assay and diagnosis. Compared with other nanoparticles, lanthanide coordination polymer nanoparticles (Ln-CPs) have been demonstrated as the excellent biomolecule sensing platforms due to their unique optical properties and intrinsic porosities. In this work, the cerium coordination polymer nanoparticles ATP-Ce-Tris were synthesized in a simple and quick way. The synthesized ATP-Ce-Tris nanoparticle shows the characteristic peak of Ce3+ located at 365 nm, which is corresponding to the 4f→5d transition of Ce3+. In the presence of Fe3+, the fluorescence of ATP-Ce-Tris quenched, and the following added ascorbic acid (AA) makes it restoring effectively. Based on this, we constructed a fluorescence probe with excellent sensitivity for AA sensing in a wide linear relationship from 0.05 to 500 μM. The detection limit was as low as 18 nM (signal-to-noise ratio of three), which is one or two orders of magnitude lower than those of reported sensors. The proposed sensing systems also exhibits excellent sensitivity for AA detection in human serum sample, exploiting a valuable platform for AA analysis in clinic diagnostic and drug screening.
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Affiliation(s)
- Hui-Hui Zeng
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Fang Liu
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Long-Ke Hu
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Jie Deng
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Yue-Ping Xie
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Wei Xiao
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Pei-Qing Lai
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Yong Wang
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Ya-Feng Feng
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
| | - Jing-Chen Yu
- Jiangxi Key Laboratory of Industrial Ceramics, Pingxiang University, Pingxiang, China
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8
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Paterson KA, Arlt J, Jones AC. Dynamic and static quenching of 2-aminopurine fluorescence by the natural DNA nucleotides in solution. Methods Appl Fluoresc 2020; 8:025002. [PMID: 32000159 DOI: 10.1088/2050-6120/ab71c3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
2-aminopurine (2AP) is a responsive fluorescent base analogue that is used widely as a probe of the local molecular environment in DNA. The ability of 2AP to report changes in local conformation and base-stacking interactions arises from the efficient quenching of its fluorescence by the natural DNA bases. However, the mechanism of this inter-base quenching remains imperfectly understood. Two previous studies of the collisional quenching of 2AP by the natural bases, in different buffer solutions, showed that dynamic quenching efficiency depends on the identity of the natural base, but disagreed on the relative quenching efficiencies of the bases. We report a comprehensive investigation of inter-base quenching of 2AP by the natural nucleoside monophosphates (NMPs), replicating the buffer conditions used in the previous studies. Using time-resolved fluorescence measurements to distinguish between dynamic and static quenching, we find that the dynamic quenching rate constants of the different bases show a consistent trend across both buffers, and this is in line with a charge-transfer mechanism. Time-resolved measurements also provide insight into static quenching, revealing formation of 2AP-NMP ground-state complexes in which 2AP displays a very short fluorescence lifetime, comparable to that seen in oligonucleotides. In these complexes, the dependence of the rate of quenching on the partner base also supports a charge-transfer mechanism.
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Affiliation(s)
- Kyle A Paterson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
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9
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Martinez-Fernandez L, Gustavsson T, Diederichsen U, Improta R. Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations. Molecules 2020; 25:E824. [PMID: 32070032 PMCID: PMC7071107 DOI: 10.3390/molecules25040824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
The fluorescent base guanine analog, 8-vinyl-deoxyguanosine (8vdG), is studied in solution using a combination of optical spectroscopies, notably femtosecond fluorescence upconversion and quantum chemical calculations, based on time-dependent density functional theory (TD-DFT) and including solvent effect by using a mixed discrete-continuum model. In all investigated solvents, the fluorescence is very long lived (3-4 ns), emanating from a stable excited state minimum with pronounced intramolecular charge-transfer character. The main non-radiative decay channel features a sizeable energy barrier and it is affected by the polarity and the H-bonding properties of the solvent. Calculations provide a picture of dynamical solvation effects fully consistent with the experimental results and show that the photophysical properties of 8vdG are modulated by the orientation of the vinyl group with respect to the purine ring, which in turn depends on the solvent. These findings may have importance for the understanding of the fluorescence properties of 8vdG when incorporated in a DNA helix.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry) Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Ulf Diederichsen
- Univ Goettingen, Inst Organ & Biomol Chem, Tammannstr 2, D-37077 Goettingen, Germany;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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10
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Levine BG, Esch MP, Fales BS, Hardwick DT, Peng WT, Shu Y. Conical Intersections at the Nanoscale: Molecular Ideas for Materials. Annu Rev Phys Chem 2019; 70:21-43. [DOI: 10.1146/annurev-physchem-042018-052425] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. After briefly introducing conical intersections, we argue that specific defects in materials can induce conical intersections between the ground and first excited electronic states, thus introducing pathways for nonradiative recombination. We present recent developments in theoretical methods, computational tools, and chemical intuition for the prediction of such defect-induced conical intersections. Through examples in various nanomaterials, we illustrate the significance of conical intersections for nanoscience. We also discuss challenges facing research in this area and opportunities for progress.
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Affiliation(s)
- Benjamin G. Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael P. Esch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - B. Scott Fales
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dylan T. Hardwick
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Wei-Tao Peng
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Yinan Shu
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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11
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Bull GD, Thompson KC. Proton Transfer and Tautomerism in 2-Aminopurine-Thymine and Pyrrolocytosine-Guanine Base Pairs. Biochemistry 2018; 57:4547-4561. [PMID: 30024730 DOI: 10.1021/acs.biochem.8b00521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T, the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T, an alternative, stable, tautomer base pair was located in the first electronically excited state; however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state, and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations.
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Affiliation(s)
- Graham D Bull
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
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12
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Nguyen QL, Spata VA, Matsika S. Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue. Phys Chem Chem Phys 2018; 18:20189-98. [PMID: 27251599 DOI: 10.1039/c6cp01559j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay.
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13
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Orr-Ewing AJ, Temps F. Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy. Phys Chem Chem Phys 2018; 20:20033-20042. [DOI: 10.1039/c8cp02664e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | - Katharina Röttger
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
- School of Chemistry
| | | | | | - Mats Bohnsack
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | | | - Friedrich Temps
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
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14
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Wang W, Sheng X, Zhang S, Huang F, Sun C, Liu J, Chen D. Theoretical insights into the structural and fluorescence properties of DNA containing fluorescent nucleobases. Phys Chem Chem Phys 2018; 20:16641-16649. [DOI: 10.1039/c8cp02295j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The structural and fluorescence properties of DNA containing fluorescent nucleobases are explored in detail. In particular, the effect of stacking with different neighboring bases on fluorescence properties is elucidated.
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Affiliation(s)
- Wenjuan Wang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Xiehuang Sheng
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Shaolong Zhang
- College of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- P. R. China
| | - Fang Huang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chuanzhi Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jianbiao Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Dezhan Chen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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15
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Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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16
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Remington JM, Philip AM, Hariharan M, Kohler B. On the origin of multiexponential fluorescence decays from 2-aminopurine-labeled dinucleotides. J Chem Phys 2017; 145:155101. [PMID: 27782452 DOI: 10.1063/1.4964718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The fluorescent probe 2-aminopurine (2Ap) has been used for decades to study local conformational fluctuations in DNA. Steady-state and time-resolved measurements of 2Ap fluorescence have been used to predict specific conformational states through suitable modeling of the quenching of the fluorescence of a 2Ap residue incorporated site-specifically into a DNA strand. The success of this approach has been limited by a lack of understanding of the precise factors responsible for the complex, multiexponential decays observed experimentally. In this study, dinucleotides composed of 2Ap and adenine were studied by the time-correlated single-photon counting technique to investigate the causes of heterogeneous emission kinetics. Contrary to previous reports, we argue that emission from 2Ap that is stacked with a neighboring base contributes negligibly to the emission signals recorded more than 50 ps after excitation, which are instead dominated by emission from unstacked 2Ap. We find that the decay kinetics can be modeled using a continuous lifetime distribution, which arises from the inherent distance dependence of electron transfer rates without the need to postulate a small number of discrete states with decay times derived from multiexponential fits. These results offer a new perspective on the quenching of 2Ap fluorescence and expand the information that can be obtained from experiments.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
| | - Abbey M Philip
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Bern Kohler
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
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17
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Kochman MA, Pola M, Miller RJD. Theoretical Study of the Photophysics of 8-Vinylguanine, an Isomorphic Fluorescent Analogue of Guanine. J Phys Chem A 2016; 120:6200-15. [DOI: 10.1021/acs.jpca.6b04723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michał A. Kochman
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Martina Pola
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
- Institut
für Theoretische Physik, Universität Hamburg, Jungiusstraße
9, 20355 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
- Department
of Chemistry and Physics, University of Toronto, 80 St. George
Street, Toronto, Ontario M5S 3H6, Canada
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18
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Spata VA, Lee W, Matsika S. Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides. J Phys Chem Lett 2016; 7:976-984. [PMID: 26911276 DOI: 10.1021/acs.jpclett.5b02756] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Wook Lee
- 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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19
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Voltz K, Léonard J, Touceda PT, Conyard J, Chaker Z, Dejaegere A, Godet J, Mély Y, Haacke S, Stote RH. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy. Nucleic Acids Res 2016; 44:3408-19. [PMID: 26896800 PMCID: PMC4838372 DOI: 10.1093/nar/gkw077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.
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Affiliation(s)
- Karine Voltz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Patricia Tourón Touceda
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Jamie Conyard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Ziyad Chaker
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
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20
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Pan L, Zhang J, Bian W. Theoretical study on the photodegradation reaction of deca-BDE in THF in the presence of furan. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1760-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
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22
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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23
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Fujikawa M, Kobayashi K, Kozawa T. Redox-dependent DNA distortion in a SoxR protein-promoter complex studied using fluorescent probes. J Biochem 2014; 157:389-97. [PMID: 25520038 DOI: 10.1093/jb/mvu085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/12/2014] [Indexed: 11/13/2022] Open
Abstract
The [2Fe-2S] transcriptional factor SoxR, a member of the MerR family, is regulated by the reversible oxidation and reduction of [2Fe-2S] clusters and functions as a sensor of oxidative stress in Escherichia coli. In the oxidized state, distortion of the target DNA promoter region initiates transcription by RNA polymerase, thereby activating transcription. The inactive reduced state of the protein has remained uncharacterized. Here, we directly observed redox-dependent conformational changes in the promoter DNA by site-specifically replacing selected adenine (A) and cytosine (C) bases in the promoter oligonucleotide with the fluorescent probes 2-aminopurine (2Ap) and pyrrolocytosine (pyrrolo-dC), respectively. Reduction of the [2Fe-2S] cluster in the SoxR-DNA complex dramatically weakened the fluorescence intensity of the 2Ap moieties incorporated into the central part of the DNA. In contrast, the fluorescence of 2Ap moieties incorporated at A in other regions and the fluorescence of pyrrolo-dC moieties in the central region of the DNA (C3 and C3') were only slightly decreased by the reduction. These results strongly suggest that the redox change causes a large conformational change within a region confined to the central A-T base pairs in the promoter region of the DNA.
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Affiliation(s)
- Mayu Fujikawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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24
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Brovarets’ OO, Yurenko YP, Hovorun DM. The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation. J Biomol Struct Dyn 2014; 33:1624-52. [DOI: 10.1080/07391102.2014.968623] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Spata VA, Matsika S. Role of excitonic coupling and charge-transfer states in the absorption and CD spectra of adenine-based oligonucleotides investigated through QM/MM simulations. J Phys Chem A 2014; 118:12021-30. [PMID: 25184994 DOI: 10.1021/jp507520c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this work, we study the photophysical properties of an adenine-based oligonucleotide using an ensemble of about 200 configurations obtained from molecular dynamics simulations. Specifically, a QM/MM approach is used to obtain the excited-state energies and properties of (dA)20(dT)20 with a dimer of π-stacked adenine bases included in the quantum region. The absorption and circular dichroism spectra are computed and analyzed using the algebraic diagrammatic construction through second order level of theory method (ADC(2)) combined with classical mechanics. We find that the experimentally observed red-shifted shoulder in the absorption spectrum is due to excitonic interactions, while charge-transfer states are present within the absorption band at the higher-energy end of the spectrum. More importantly, low-energy states with charge-transfer mixing exist, which could lead to excimers and bonded excimers. These observations suggest that mixing between charge-transfer and excitonic states plays an important role in the photophysics of oligonucleotides. They also highlight the importance of taking into account the conformational flexibility of the oligonucleotide when investigating photophysical properties.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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26
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Vaganova E, Wachtel E, Leitus G, Danovich D, Popov I, Dubnikova F, Yitzchaik S. Blue-violet photoluminescence of 4-isopropyl-pyridine hydroxide crystals. J Phys Chem A 2014; 118:3061-7. [PMID: 24708153 DOI: 10.1021/jp411879j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is continuing interest in determining essential structural features of polymer gels, which display photoelectric and/or thermoelectric behavior. One such gel is the blend, poly(4-vinylpyridine-co-butyl methacrylate)/poly(4-vinylpyridine), dissolved in liquid pyridine. Following extended aeration of a three-component mixture, which serves as a model for the gel side chain interactions, crystallization of a new molecule, 4-isopropylpyridine hydroxide (IPPOH), occurs. X-ray diffraction, DFT modeling, and spectroscopy were used to determine the structural, electronic, and luminescent properties of the crystal. The crystal structure reveals molecules forming head-to-tail, hydrogen-bonded chains without base stacking or marked interchain interaction. The molecular chains are characterized by moderately long-lived, blue-violet luminescence excited in the near-UV. Because these photoluminescent properties resemble those of the gel from which the crystals are derived, we may posit similar structural features in the gel for which direct structural analysis is not available.
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Affiliation(s)
- Evgenia Vaganova
- Institute of Chemistry, The Hebrew University of Jerusalem , Givat Ram, 91904 Jerusalem, Israel
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27
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Mohapatra B, Verma S. Crystallographic Studies of Modified 2-Aminopurine Nucleobase with Transition Metal Ions. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2014. [DOI: 10.1007/s40010-014-0147-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Dziuba D, Karpenko IA, Barthes NPF, Michel BY, Klymchenko AS, Benhida R, Demchenko AP, Mély Y, Burger A. Rational Design of a Solvatochromic Fluorescent Uracil Analogue with a Dual-Band Ratiometric Response Based on 3-Hydroxychromone. Chemistry 2014; 20:1998-2009. [DOI: 10.1002/chem.201303399] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/24/2022]
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29
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30
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West BA, Molesky BP, Giokas PG, Moran AM. Uncovering molecular relaxation processes with nonlinear spectroscopies in the deep UV. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Liang J, Nguyen QL, Matsika S. Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases. Photochem Photobiol Sci 2013; 12:1387-400. [PMID: 23625036 PMCID: PMC5006741 DOI: 10.1039/c3pp25449f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 03/29/2013] [Indexed: 12/26/2022]
Abstract
Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids' structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.
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Affiliation(s)
- JingXin Liang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Quynh L. Nguyen
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
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32
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Spata VA, Matsika S. Bonded Excimer Formation in π-Stacked 9-Methyladenine Dimers. J Phys Chem A 2013; 117:8718-28. [DOI: 10.1021/jp4033194] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vincent A. Spata
- 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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33
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Pan L, Bian W, Zhang J. The Effect of Explicit Solvent on Photodegradation of Decabromodiphenyl Ether in Toluene: Insights from Theoretical Study. J Phys Chem A 2013; 117:5291-8. [DOI: 10.1021/jp403958g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu Pan
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wensheng Bian
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiaxu Zhang
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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34
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Abou-Zied OK. Effect of NH2 rotation on the fluorescence of 2-aminopurine in solution. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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35
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Blindauer CA, Sigel A, Operschall BP, Holý A, Sigel H. Extent of Intramolecular π Stacks in Aqueous Solution in Mixed-Ligand Copper(II) Complexes Formed by Heteroaromatic Amines and 1-[2-(Phosphonomethoxy)ethyl]cytosine (PMEC), a Relative of Antivirally Active Acyclic Nucleotide Analogues (Part 72) [1, 2]. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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36
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Gómez-Coca RB, Blindauer CA, Sigel A, Operschall BP, Holý A, Sigel H. Extent of intramolecular π-stacks in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and several 2-aminopurine derivatives of the antivirally active nucleotide analog 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). Chem Biodivers 2013; 9:2008-34. [PMID: 22976988 DOI: 10.1002/cbdv.201200022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The acidity constants of twofold protonated, antivirally active, acyclic nucleoside phosphonates (ANPs), H(2)(PE)(±), where PE(2-)=9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)), 2-amino-9-[2-(phosphonomethoxy)ethyl]purine (PME2AP(2-)), 2,6-diamino-9-[2-(phosphonomethoxy)ethyl]purine (PMEDAP(2-)), or 2-amino-6-(dimethylamino)-9-[2-(phosphonomethoxy)ethyl]purine (PME(2A6DMAP)(2-)), as well as the stability constants of the corresponding ternary Cu(Arm)(H;PE)(+) and Cu(Arm)(PE) complexes, where Arm=2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen), are compared. The constants for the systems containing PE(2-)=PMEDAP(2-) and PME(2A6DMAP)(2-) have been determined now by potentiometric pH titrations in aqueous solution at I=0.1M (NaNO(3)) and 25°; the corresponding results for the other ANPs were taken from our earlier work. The basicity of the terminal phosphonate group is very similar for all the ANP(2-) species, whereas the addition of a second amino substituent at the pyrimidine ring of the purine moiety significantly increases the basicity of the N(1) site. Detailed stability-constant comparisons reveal that, in the monoprotonated ternary Cu(Arm)(H;PE)(+) complexes, the proton is at the phosphonate group, that the ether O-atom of the -CH(2)-O-CH(2)-P(O)(2)(-)(OH) residue participates, next to the P(O)(2)(-)(OH) group, to some extent in Cu(Arm)(2+) coordination, and that π-π stacking between the aromatic rings of Cu(Arm)(2+) and the purine moiety is rather important, especially for the H·PMEDAP(-) and H·PME(2A6DMAP)(-) ligands. There are indications that ternary Cu(Arm)(2+)-bridged stacks as well as unbridged (binary) stacks are formed. The ternary Cu(Arm)(PE) complexes are considerably more stable than the corresponding Cu(Arm)(R-PO(3)) species, where R-PO(3)(2-) represents a phosph(on)ate ligand with a group R that is unable to participate in any kind of intramolecular interaction within the complexes. The observed stability enhancements are mainly attributed to intramolecular-stack formation in the Cu(Arm)(PE) complexes and also, to a smaller extent, to the formation of five-membered chelates involving the ether O-atom present in the -CH(2)-O-CH(2)-PO(3)(2-) residue of the PE(2-) species. The quantitative analysis of the intramolecular equilibria involving three structurally different Cu(Arm)(PE) isomers shows that, e.g., ca. 1.5% of the Cu(phen)(PMEDAP) system exist with Cu(phen)(2+) solely coordinated to the phosphonate group, 4.5% as a five-membered chelate involving the ether O-atom of the -CH(2)-O-CH(2)-PO(3)(2-) residue, and 94% with an intramolecular π-π stack between the purine moiety of PMEDAP(2-) and the aromatic rings of phen. Comparison of the various formation degrees of the species formed reveals that, in the Cu(phen)(PE) complexes, intramolecular-stack formation is more pronounced than in the Cu(bpy)(PE) species. Within a given Cu(Arm)(2+) series the stacking intensity increases in the order PME2AP(2-) <PMEA(2-) <PMEDAP(2-) <PME(2A6DMAP)(2-). One could speculate that the reduced stacking intensity of PME2AP(2-), together with a different H-bonding pattern, could well lead to a different orientation of the 2-aminopurine moiety (compared to the adenine residue) in the active site of nucleic acid polymerases and thus be responsible for the reduced antiviral activity of PME2AP compared with that of PMEA and the other ANPs containing a 6-amino substituent.
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Affiliation(s)
- Raquel B Gómez-Coca
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel
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Tan Y, Yu J, Gao J, Cui Y, Wang Z, Yang Y, Qian G. A fluorescent pH chemosensor for strongly acidic conditions based on the intramolecular charge transfer (ICT) effect. RSC Adv 2013. [DOI: 10.1039/c3ra00120b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Oxidation and reduction potentials of 8-vinyladenosine measured by cyclic voltammetry: Implications for photoinduced electron transfer quenching of a fluorescent adenine analog. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rankin KM, Sproviero M, Rankin K, Sharma P, Wetmore SD, Manderville RA. C8-heteroaryl-2'-deoxyguanosine adducts as conformational fluorescent probes in the NarI recognition sequence. J Org Chem 2012; 77:10498-508. [PMID: 23171213 DOI: 10.1021/jo302164c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The optical, redox, and electronic properties of C(8)-heteroaryl-2'-deoxyguanosine (dG) adducts with C(8)-substituents consisting of furyl ((Fur)dG), pyrrolyl ((Pyr)dG), thienyl ((Th)dG), benzofuryl ((Bfur)dG), indolyl ((Ind)dG), and benzothienyl ((Bth)dG) are described. These adducts behave as fluorescent nucleobase probes with emission maxima from 379 to 419 nm and fluorescence quantum yields (Φ(fl)) in the 0.1-0.8 range in water at neutral pH. The probes exhibit quenched fluorescence with increased solvent viscosity and decreased solvent polarity. The (Fur)dG, (Bfur)dG, (Ind)dG, and (Bth)dG derivatives were incorporated into the G(3) position of the 12-mer oligonucleotide 5'-CTCG(1)G(2)CG(3)CCATC-3' that contains the recognition sequence of the NarI Type II restriction endonuclease. This sequence is widely used to study the biological activity (mutagenicity) of C(8)-arylamine-dG adducts with adduct conformation (anti vs syn) playing a critical role in the biological outcome. The modified NarI(X = (Fur)G, (Ind)G, (Bfur)G, or (Bth)G) oligonucleotides were hybridized to the complementary strand containing either C (NarI'(C)) or G (NarI'(G)) opposite the probe. The duplex structures were characterized by UV melting temperature analysis, fluorescence spectroscopy, collisional fluorescence quenching studies, and circular dichroism (CD). The emission of the probes showed sensitivity to the opposing base in the duplex, and suggested the utility of fluorescence spectroscopy to monitor probe conformation.
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Affiliation(s)
- Katherine M Rankin
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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West BA, Womick JM, Moran AM. Interplay between vibrational energy transfer and excited state deactivation in DNA components. J Phys Chem A 2012; 117:5865-74. [PMID: 22920964 DOI: 10.1021/jp306799e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Femtosecond laser spectroscopies are used to examine a thymine family of systems chosen to expose the interplay between excited state deactivation and two distinct vibrational energy transfer (VET) pathways: (i) VET from the base to the deoxyribose ring; (ii) VET between neighboring units in a dinucleotide. We find that relaxation in the ground electronic state accelerates markedly as the molecular sizes increase from the nucleobase to the dinucleotide. This behavior directly reflects growth in the density of vibrational quantum states on the substituent of the base. Excited state lifetimes are studied at temperatures ranging from 100 to 300 K to characterize the thermal fluctuations that connect the Franck-Condon geometries and the conical intersections leading back to the ground state. An Arrhenius analysis yields an approximate excited state energy barrier of 13 meV in the thymine dinucleotide. In addition, we find that the transfer of vibrational energy from the base to the substituent suppresses thermal fluctuations across this energy barrier. The possibility that the solvent viscosity imposes friction on the reaction coordinate is examined by comparing thymine and adenine systems. Experiments suggest that the solvent viscosity has little effect on barrier crossing dynamics in thymine because the conical intersection is accessed through relatively small out-of-plane atomic displacements. Overall, we conclude that the transfer of vibrational quanta from thymine to the deoxyribose ring couples significantly to the internal conversion rate, whereas the neighboring unit in the dinucleotide serves as a secondary heat bath. In natural DNA, it follows that (local) thermal fluctuations in the geometries of subunits involving the base and deoxyribose ring are most important to this subpicosecond relaxation process.
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Affiliation(s)
- Brantley A West
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Dierckx A, Miannay FA, Ben Gaied N, Preus S, Björck M, Brown T, Wilhelmsson LM. Quadracyclic adenine: a non-perturbing fluorescent adenine analogue. Chemistry 2012; 18:5987-97. [PMID: 22437923 DOI: 10.1002/chem.201103419] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Indexed: 12/26/2022]
Abstract
Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Gothenburg, Sweden
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Kodali G, Narayanan M, Stanley RJ. Excited-state electronic properties of 6-methylisoxanthopterin (6-MI): an experimental and theoretical study. J Phys Chem B 2012; 116:2981-9. [PMID: 22276652 DOI: 10.1021/jp2110083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Methylisoxanthopterin (6-MI) is a pteridine-based guanine analog that has a red-shifted absorption and high fluorescence quantum yield. Its Watson-Crick base-pairing and base stacking properties are similar to guanine. The fluorescence quantum yield of 6-MI is sensitive to its nearest neighbors and base stacking, making it a very useful real-time probe of DNA structure. The fundamental photophysics underlying this fluorescence quenching by base stacking is not well understood. We have explored the excited-state electronic structure of the 6-MI in frozen 77 K LiCl glasses using Stark spectroscopy. These measurements yielded the direction and degree of charge redistribution for the S(0)→S(1) transition as manifested in the difference dipole moment, Δμ(01), and difference static polarizability, TrΔα. TDDFT (time-dependent density functional theory) was employed to calculate the transition energy, oscillator strength, and the dipole moments of the ground and lowest optically bright excited state of 6-MI (S(0)→S(1)). The direction of Δμ(01) was assigned in the molecular frame based on the Stark data and calculations. These results suggest that the C4═O and C2-NH(2) groups are electron-deficient in the excited state, a very different outcome compared with guanine. This implies that Watson-Crick hydrogen bonding in 6-MI may be modulated by absorption of a photon so as to strengthen base pairing, if only transiently. Solvatochromism was also obtained for the absorption and emission spectra of 6-MI in various solvents and compared with the Stark spectroscopic results using both the Lippert-Mataga and Bakhshiev models.
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Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Sigel A, Operschall BP, Sigel H. Steric guiding of metal ion binding to a purine residue by a non-coordinating amino group: Examplified by 9-[(2-phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer of the antiviral nucleotide analogue 9-[(2-phosphonomethoxy)ethyl]adenine (PMEA), and by related compounds. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.06.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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West BA, Womick JM, Moran AM. Influence of temperature on thymine-to-solvent vibrational energy transfer. J Chem Phys 2011; 135:114505. [DOI: 10.1063/1.3628451] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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