1
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Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
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Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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2
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Beal R, Valverde D, Gonçalvez PFB, Borin AC. Photophysics of tz Adenine and tz Guanine fluorescent nucleobases embedded into DNA and RNA. J Comput Chem 2023; 44:2246-2255. [PMID: 37486177 DOI: 10.1002/jcc.27194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
UV-VIS photoinduced events of tz A and tz G embedded into DNA and RNA are described by combining the Extended Multi-State Second-Order Perturbation Theory (XMS-CASPT2) and electrostatic embedding molecular mechanics methods (QM/MM). Our results point out that the S1 1 (ππ* La ) state is the bright state in both environments. After the photoexcitation to the S1 1 (ππ* La ) state, the electronic population evolves barrierless towards its minimum, from where the excess of energy can be dissipated by fluorescence. As the minimum energy crossing point structure between the ground and first bright states lies in a high-energy region, the direct internal conversion to the ground state is an unviable mechanism. Other spectroscopic properties (for instance, absorption and Stokes shifts) and comparisons with photochemical properties of canonical nucleobases are also provided.
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Affiliation(s)
- Roiney Beal
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Paulo F B Gonçalvez
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
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3
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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4
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Franco LR, Toledo KCF, Matias TA, Benavides PA, Cezar HM, Araujo CM, Coutinho K, Araki K. Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand. Phys Chem Chem Phys 2022; 24:10222-10240. [PMID: 35420602 DOI: 10.1039/d1cp03912a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interactions and the solvent effects on the distribution of several species in equilibrium and how it can influence the 1H-NMR properties, spectroscopy (UV-vis absorption), and the acid-base equilibria can be especially challenging. This is the case of a bis-bidentate bridging ligand bis(2-pyridyl)-benzo-bis(imidazole), where the two pyridyl and four imidazolyl nitrogen atoms can be protonated in different ways, depending on the solvent, generating many isomeric/tautomeric species. Herein, we report a combined theoretical-experimental approach based on a sequential quantum mechanics/molecular mechanics procedure that was successfully applied to describe in detail the acid-base characterization and its effects on the electronic properties of such a molecule in solution. The calculated free-energies allowed the identification of the main species present in solution as a function of the solvent polarity, and its effects on the magnetic shielding of protons (1H-NMR chemical shifts), the UV-vis absorption spectra, and the acid-base equilibrium constants (pKas) in aqueous solution. Three acid-base equilibrium constants were experimentally/theoretically determined (pKa1 = 1.3/1.2, pKa2 = 2.1/2.2 and pKa5 = 10.1/11.3) involving mono-deprotonated and mono-protonated cis and trans species. Interestingly, other processes with pKa3 = 3.7 and pKa4 = 6.0 were also experimentally determined and assigned to the protonation and deprotonation of dimeric species. The dimerization of the most stable neutral species was investigated by Monte Carlo simulations and its electronic effects were considered for the elucidation of the UV-vis absorption bands, revealing transitions mainly with the charge-transfer characteristic and involving both the monomeric species and the dimeric species. The good matching of the theoretical and experimental results provides an atomistic insight into the solvent effects on the electronic properties of this bis-bidentate bridging ligand.
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Affiliation(s)
- Leandro Rezende Franco
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil. .,Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden
| | | | - Tiago Araujo Matias
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
| | - Paola Andrea Benavides
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
| | - Henrique Musseli Cezar
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil.
| | - C Moyses Araujo
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.,Materials Theory Division, Department of Physics and Astronomy, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil.
| | - Koiti Araki
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
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5
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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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6
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Sanches de Araújo AV, Valverde D, Canuto S, Borin AC. Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tzA, tzG, and tzI. J Phys Chem A 2020; 124:6834-6844. [PMID: 32786984 DOI: 10.1021/acs.jpca.0c03398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The photophysical relaxation pathways of tzA, tzG, and tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying 1(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the 1(ππ*)min region, the conical intersection with the ground state ((ππ*/GS)CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.
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Affiliation(s)
| | - Danillo Valverde
- Institute of Physics, University of São Paulo, Rua do Matão 1371, 05508-090 São Paulo, SP, Brazil
| | - Sylvio Canuto
- Institute of Physics, University of São Paulo, Rua do Matão 1371, 05508-090 São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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7
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Xue Y, Liu Y, Wang G, An L, Teng Y, Chen M, Xie Y, Zhang L. TDDFT study on the photophysical properties of coumarinyl chalcones and sensing mechanism of a derived fluorescent probe for hydrogen sulfide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 234:118263. [PMID: 32203689 DOI: 10.1016/j.saa.2020.118263] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
Coumarin-chalcone hybrids have attracted much attention in recent years due to their important optical properties. Herein, the photophysical properties of a series of coumarinyl chalcones and the sensing mechanism for H2S of a related fluorescent probe CC-DNP were investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The predicted spectral properties agree well with the experimental results, which allowed an assignment of the spectra. Our calculations successfully clarified the experimental observed fluorescence "off-on" effect and the fluorescent quenching mechanism of the probe. The results revealed that the first excited state (S1) of the probe CC-DNP is a dark state with obvious charge transfer from coumarin unit to 2,4-dinitrophenyl (DNP) moiety, which results in the fluorescence quenching via the nonradiative photoinduced electron transfer (PET) process. On the other hand, the excited state S1 in the thiolysis product CC-OH decayed directly to S0, and thus the fluorescence is recovered.
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Affiliation(s)
- Yunsheng Xue
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China.
| | - Yunping Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Guirong Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Lin An
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Yangxin Teng
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Mohan Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Yuxin Xie
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Ling Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China.
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8
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Teles‐Ferreira DC, Conti I, Borrego‐Varillas R, Nenov A, Van Stokkum IHM, Ganzer L, Manzoni C, Paula AM, Cerullo G, Garavelli M. A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils. Chemistry 2019; 26:336-343. [DOI: 10.1002/chem.201904541] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Danielle Cristina Teles‐Ferreira
- Departamento de Física Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil
- Electrical Engineering Department Federal Institute of Minas Gerais Formiga MG Brazil
| | - Irene Conti
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Rocío Borrego‐Varillas
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Ivo H. M. Van Stokkum
- Department of Physics and Astronomy Faculty of Sciences Vrije Universiteit Amsterdam De Boelelaan 1081 1081HV Amsterdam The Netherlands
| | - Lucia Ganzer
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Cristian Manzoni
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Ana Maria Paula
- Departamento de Física Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil
| | - Giulio Cerullo
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
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9
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Valverde D, Sanches de Araujo AV, Canuto S, Borin AC. Photophysics of Emissive
tz
C[Isothiazolo‐Cytidine] and
tz
U[Isothiazolo‐Uridine] Pyrimidine Analogues. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Danillo Valverde
- Institute of PhysicsUniversity of São Paulo Rua do Matão 1371 São Paulo, SP 05508-090 Brazil
| | | | - Sylvio Canuto
- Institute of PhysicsUniversity of São Paulo Rua do Matão 1371 São Paulo, SP 05508-090 Brazil
| | - Antonio Carlos Borin
- Department of Fundamental ChemistryInstitute of ChemistryUniversity of São Paulo Avenida Professor Lineu Prestes, 748 São Paulo SP, 05508-000 Brazil
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10
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Teppang KL, Lee RW, Burns DD, Turner MB, Lokensgard ME, Cooksy AL, Purse BW. Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing. Chemistry 2018; 25:1249-1259. [PMID: 30338571 DOI: 10.1002/chem.201803653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/07/2022]
Abstract
The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tCO ) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tCO compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.
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Affiliation(s)
- Kristine L Teppang
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Raymond W Lee
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Dillon D Burns
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - M Benjamin Turner
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Melissa E Lokensgard
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Andrew L Cooksy
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Byron W Purse
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
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