1
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Saintomé C, Monfret O, Doisneau G, Guianvarc'h D. Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling. Chembiochem 2024:e202400097. [PMID: 38703401 DOI: 10.1002/cbic.202400097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.
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Affiliation(s)
- Carole Saintomé
- Sorbonne Université, UFR 927, MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005, Paris, France
| | - Océane Monfret
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Gilles Doisneau
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
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2
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Navarrete-Miguel M, Giussani A, Rubio M, Boggio-Pasqua M, Borin AC, Roca-Sanjuán D. Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil. J Phys Chem A 2024; 128:2273-2285. [PMID: 38504122 PMCID: PMC10982997 DOI: 10.1021/acs.jpca.3c06310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/16/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy. This study has been carried out by determining the most favorable deactivation paths of UV-vis photoexcited 4-thiouracil by means of the photochemical reaction path approach and an efficient combination of the complete-active-space second-order perturbation theory//complete-active-space self-consistent field (CASPT2//CASSCF), (CASPT2//CASPT2), time-dependent density functional theory (TDDFT), and spin-flip TDDFT (SF-TDDFT) methodologies. By comparing the data computed herein for both 4-thiouracil and 2-thiouracil, a rationale is provided on the relatively higher yields of intersystem crossing, triplet lifetime and singlet oxygen production of 4-thiouracil, and the relatively higher yield of phosphorescence of 2-thiouracil.
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Affiliation(s)
- Miriam Navarrete-Miguel
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Angelo Giussani
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Mercedes Rubio
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Martial Boggio-Pasqua
- Laboratoire
de Chimie et Physique Quantiques, IRSAMC,
CNRS et Université Toulouse 3, 118 route de Narbonne, 31062 Toulouse, France
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry,
University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo CEP 05508-000, Brazil
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
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3
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Sato R, Yamada Y, Kashihara W, Nishihara T, Tanabe K, Xu YZ, Suzuki T. Excited state properties of 5-fluoro-4-thiouridine derivative †. Photochem Photobiol 2024; 100:434-442. [PMID: 38312100 DOI: 10.1111/php.13918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/06/2024]
Abstract
The excited state properties of thionated 5-fluorouridine (2',3',5'-tri-O-acetyl-5-fluoro-4-thiouridine; ta5F4TUrd), synthesized with Lawesson's reagent, have been intensively investigated with nanosecond transient absorption spectroscopy, time-resolved thermal lensing, near-infrared emission, and quantum chemical calculation. The intrinsic triplet lifetime of ta5F4TUrd was determined to be4.2 ± 0.7 μs in acetonitrile, and the formation quantum yield of the excited triplet state was as large as0.79 ± 0.01 . The quenching rate constants of the triplet ta5F4TUrd by the dissolved oxygen molecule and by the self-quenching process were found to be nearly equal to the diffusion-controlled rate of acetonitrile. The quantum yield of the singlet molecular oxygen produced through energy transfer between the triplet ta5F4TUrd and the dissolved oxygen,Φ Δ , was successfully determined to be0.61 ± 0.02 under the oxygen-saturated condition. From the oxygen concentration dependence of theΦ Δ value, the fraction of triplet ta5F4TUrd quenched by dissolved oxygen which gives rise to the 1 O2 * formation,S Δ , was successfully obtained to be0.78 ± 0.01 , which was the largest among the thionucleobases and the thionucleosides reported so far. This could be due to the lower energy and/or the ππ* character of the triplet state.
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Affiliation(s)
- Rin Sato
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Yoshino Yamada
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Wataru Kashihara
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Tatsuya Nishihara
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Yao-Zhong Xu
- School of Life, Health and Chemical Sciences, The Open University, Keynes, UK
| | - Tadashi Suzuki
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
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4
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Barr J, Colpaert G, Cadoni E, Madder A. Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting. Methods 2023; 218:189-197. [PMID: 37597698 DOI: 10.1016/j.ymeth.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Oligonucleotides (ODNs) find applications as diagnostic and therapeutic tools due to their unique ability to interact, thanks to Watson-Crick base pairing, with a specific DNA or RNA target strand. Although most of the tools available today rely on mere hydrogen bond formation, chemical modifications to enable covalent interstrand-crosslinking (ICL) have been reported, and are gaining a place under the spotlight as they potentially offer a series of advantages over the state of the art, including a higher potency and selectivity. This methodological paper focuses on the use of a pro-reactive furan moiety and its subsequent oxidation for applications in ODN targeting. The design of effective capture and targeting probes to ensure high ICL yields is discussed and the mechanisms underlying the (photo)chemical oxidation of furan are explained. Furthermore, examples of furan-containing DNAs designed for different applications, including DNA-DNA or DNA-RNA ICL and DNA-peptide/protein targeting, are provided. The paper highlights the advantages of using different oxidative chemical triggers, such as N-bromosuccinimide or singlet oxygen, to offer additional selectivity control over the ICL reaction.
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Affiliation(s)
- Jack Barr
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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5
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Ortiz-Rodríguez LA, Fang YG, Niogret G, Hadidi K, Hoehn SJ, Folkwein HJ, Jockusch S, Tor Y, Cui G, Levi L, Crespo-Hernández CE. Thieno[3,4- d]pyrimidin-4(3 H)-thione: an effective, oxygenation independent, heavy-atom-free photosensitizer for cancer cells. Chem Sci 2023; 14:8831-8841. [PMID: 37621444 PMCID: PMC10445467 DOI: 10.1039/d3sc02592f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
All-organic, heavy-atom-free photosensitizers based on thionation of nucleobases are receiving increased attention because they are easy to make, noncytotoxic, work both in the presence and absence of molecular oxygen, and can be readily incorporated into DNA and RNA. In this contribution, the DNA and RNA fluorescent probe, thieno[3,4-d]pyrimidin-4(1H)-one, has been thionated to develop thieno[3,4-d]pyrimidin-4(3H)-thione, which is nonfluorescent and absorbs near-visible radiation with about 60% higher efficiency. Steady-state absorption and emission spectra are combined with transient absorption spectroscopy and CASPT2 calculations to delineate the electronic relaxation mechanisms of both pyrimidine derivatives in aqueous and acetonitrile solutions. It is demonstrated that thieno[3,4-d]pyrimidin-4(3H)-thione efficiently populates the long-lived and reactive triplet state generating singlet oxygen with a quantum yield of about 80% independent of solvent. It is further shown that thieno[3,4-d]pyrimidin-4(3H)-thione exhibits high photodynamic efficacy against monolayer melanoma cells and cervical cancer cells both under normoxic and hypoxic conditions. Our combined spectroscopic, computational, and in vitro data demonstrate the excellent potential of thieno[3,4-d]pyrimidin-4(1H)-thione as a heavy-atom-free PDT agent and paves the way for further development of photosensitizers based on the thionation of thieno[3,4-d]pyrimidine derivatives. Collectively, the experimental and computational results demonstrate that thieno[3,4-d]pyrimidine-4(3H)-thione stands out as the most promising thiobase photosensitizer developed to this date.
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Affiliation(s)
| | - Ye-Guang Fang
- Key Lab of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University Beijing 100875 China
| | - Germain Niogret
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Kaivin Hadidi
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University Cleveland OH 44106 USA
| | - Heather J Folkwein
- Department of Chemistry, Case Western Reserve University Cleveland OH 44106 USA
| | - Steffen Jockusch
- Center for Photochemical Sciences, Bowling Green State University Bowling Green Ohio 43403 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Ganglong Cui
- Key Lab of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University Beijing 100875 China
| | - Liraz Levi
- Celloram Inc Cleveland OH 44106 USA
- Department of Pediatrics, Case Western Reserve University School of Medicine Cleveland Ohio 44106 USA
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6
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Yeter-Alat H, Belgareh-Touzé N, Huvelle E, Banroques J, Tanner NK. The DEAD-Box RNA Helicase Ded1 Is Associated with Translating Ribosomes. Genes (Basel) 2023; 14:1566. [PMID: 37628617 PMCID: PMC10454743 DOI: 10.3390/genes14081566] [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: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. We used a modified PAR-CLIP technique, which we call quicktime PAR-CLIP (qtPAR-CLIP), to crosslink Ded1 to 4-thiouridine-incorporated RNAs in vivo using UV light centered at 365 nm. The irradiation conditions are largely benign to the yeast cells and to Ded1, and we are able to obtain a high efficiency of crosslinking under physiological conditions. We find that Ded1 forms crosslinks on the open reading frames of many different mRNAs, but it forms the most extensive interactions on relatively few mRNAs, and particularly on mRNAs encoding certain ribosomal proteins and translation factors. Under glucose-depletion conditions, the crosslinking pattern shifts to mRNAs encoding metabolic and stress-related proteins, which reflects the altered translation. These data are consistent with Ded1 functioning in the regulation of translation elongation, perhaps by pausing or stabilizing the ribosomes through its ATP-dependent binding.
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Affiliation(s)
- Hilal Yeter-Alat
- Expression Génétique Microbienne, Université de Paris Cité & CNRS, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (E.H.); (J.B.)
- Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, CNRS UMR8261, EGM, 75005 Paris, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226 CNRS, Institut de Biologie Physico-Chimique, Sorbonne Université, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
| | - Emmeline Huvelle
- Expression Génétique Microbienne, Université de Paris Cité & CNRS, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (E.H.); (J.B.)
- Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, CNRS UMR8261, EGM, 75005 Paris, France
| | - Josette Banroques
- Expression Génétique Microbienne, Université de Paris Cité & CNRS, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (E.H.); (J.B.)
- Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, CNRS UMR8261, EGM, 75005 Paris, France
| | - N. Kyle Tanner
- Expression Génétique Microbienne, Université de Paris Cité & CNRS, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (E.H.); (J.B.)
- Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, CNRS UMR8261, EGM, 75005 Paris, France
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7
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Velema WA, Lu Z. Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications. JACS AU 2023; 3:316-332. [PMID: 36873678 PMCID: PMC9975857 DOI: 10.1021/jacsau.2c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.
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Affiliation(s)
- Willem A. Velema
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6500 HC, The Netherlands
| | - Zhipeng Lu
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
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8
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Krancewicz K, Koput J, Hug GL, Marciniak B, Taras-Goslinska KM. Unusual photophysical properties of a new tricyclic derivative of thiopurines in terms of potential applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121620. [PMID: 35853257 DOI: 10.1016/j.saa.2022.121620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The thio analogues of purine bases have been found to possess notable biological and pharmacological capabilities and have an important role to play as anticancer and immunosuppressive drugs. In this work a new tricyclic analogue of guanosine containing sulfur was synthesized, in particular, DTEG (2',3',5'-tri-O-acetyl-6,9-dithioethanoguanosine). Although there is promise for thiopurine derivatives for biomedical applications, there are some liabilities in regard to their exposure to light. As a preliminary survey for such difficulties with DTEG, this work looks into spectral and photophysical processes of DTEG using time-resolved and steady-state optical excitation. In contrast to other thiopurines, which have long-lived triplets, DTEG is shown to have a short-lived triplet making it less dangerous for singlet-oxygen sensitization. Even in anaerobic solutions, its photoreactivity is negligible. These various unusual photochemical properties of DTEG are consistent with DTEG being very promising as an alternative drug to the currently used 6-thiopurines. DTEG also has some interesting photophysical behavior that is distinct from other thioketones. Although thioketones have an unusual fluorescence violating Kasha's Rule and emitting from the second excited singlet state, DTEG does this also, but, in addition, it shows dual fluorescence by emitting from its first excited singlet as well. The assignments of the nature of these excited states are supported by DFT results. This theory and associated kinetic analysis show quantitatively that the dual fluorescence is, in part, tied to the relatively fast S2 to S1 internal conversion compared to other S2 decays and, in part, tied to the relatively slow nonradiative decay of S1 itself.
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Affiliation(s)
| | - Jacek Koput
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Gordon L Hug
- Radiation Laboratory, University of Notre Dame, Notre Dame 46556, USA
| | - Bronisław Marciniak
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland; Centre for Advanced Technology, Adam Mickiewicz University, 61-614 Poznan, Poland
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9
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Kunkler CN, Schiefelbein GE, O'Leary NJ, McCown PJ, Brown JA. A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix. RNA (NEW YORK, N.Y.) 2022; 28:1172-1184. [PMID: 35820700 PMCID: PMC9380742 DOI: 10.1261/rna.079244.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could regulate the formation of these triple helices is through RNA modifications. With over 140 naturally occurring RNA modifications, we hypothesize that some modifications stabilize RNA•DNA-DNA triple helices while others destabilize them. Here, we focus on a pyrimidine-motif triple helix composed of canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays and microscale thermophoresis to examine how 11 different RNA modifications at a single position in an RNA•DNA-DNA triple helix affect stability: 5-methylcytidine (m5C), 5-methyluridine (m5U or rT), 3-methyluridine (m3U), pseudouridine (Ψ), 4-thiouridine (s4U), N 6-methyladenosine (m6A), inosine (I), and each nucleobase with 2'-O-methylation (Nm). Compared to the unmodified U•A-T base triple, some modifications have no significant change in stability (Um•A-T), some have ∼2.5-fold decreases in stability (m5U•A-T, Ψ•A-T, and s4U•A-T), and some completely disrupt triple helix formation (m3U•A-T). To identify potential biological examples of RNA•DNA-DNA triple helices controlled by an RNA modification, we searched RMVar, a database for RNA modifications mapped at single-nucleotide resolution, for lncRNAs containing an RNA modification within a pyrimidine-rich sequence. Using electrophoretic mobility shift assays, the binding of DNA-DNA to a 22-mer segment of human lncRNA Al157886.1 was destabilized by ∼1.7-fold with the substitution of m5C at known m5C sites. Therefore, the formation and stability of cellular RNA•DNA-DNA triple helices could be influenced by RNA modifications.
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Affiliation(s)
- Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Grace E Schiefelbein
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Phillip J McCown
- Michigan Medicine, Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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10
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Caldero-Rodríguez NE, Arpa EM, Cárdenas DJ, Martínez-Fernández L, Jockusch S, Seth SK, Corral I, Crespo-Hernández CE. 2-Oxopurine Riboside: A Dual Fluorescent Analog and Photosensitizer for RNA/DNA Research. J Phys Chem B 2022; 126:4483-4490. [PMID: 35679327 DOI: 10.1021/acs.jpcb.2c01113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
There is significant interest in developing suitable nucleoside analogs exhibiting high fluorescence and triplet yields to investigate the structure, dynamics, and binding properties of nucleic acids and promote selective photosensitized damage to DNA/RNA, respectively. In this study, steady-state, laser flash photolysis, time-resolved IR luminescence, and femtosecond broad-band transient absorption spectroscopies are combined with quantum chemical calculations to elucidate the excited-state dynamics of 2-oxopurine riboside in aqueous solution and to investigate its prospective use as a fluorescent or photosensitizer analog. The Franck-Condon population in the S1 (ππ*) state decays through a combination of solvent and conformational relaxation to its minimum in 1.9 ps. The population trapped in the 1ππ* minimum bifurcates to either fluoresce or intersystem cross to the triplet manifold within ca. 5 ns, while another fraction of the population decays nonradiatively to the ground state. It is demonstrated that 2-oxopurine riboside exhibits both high fluorescent (48%) and significant triplet (between 10% and 52%) yields, leading to a yield of singlet oxygen generation of 10%, making this nucleoside analog a dual fluorescent and photosensitizer analog for DNA and RNA research.
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Affiliation(s)
| | - Enrique M Arpa
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain
| | - Diego J Cárdenas
- Departamento de Química Orgánica, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lara Martínez-Fernández
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Steffen Jockusch
- Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Sourav Kanti Seth
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Inés Corral
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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11
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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12
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Günsel A, Yıldırım A, Taslimi P, Erden Y, Taskin-Tok T, Pişkin H, Bilgiçli AT, Gülçin İ, Nilüfer Yarasir M. Cytotoxicity effects and biochemical investigation of novel tetrakis-phthalocyanines bearing 2-thiocytosine moieties with molecular docking studies. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Dong J, Huang C, Guo S, Xia Y, Hou Y, Yang C, Zhang X, Jie J, Zhu BZ, Su H. Free-Radical-Mediated Photoinduced Electron Transfer between 6-Thioguanine and Tryptophan Leading to DNA-Protein-Like Cross-Link. J Phys Chem B 2021; 126:14-22. [PMID: 34951313 DOI: 10.1021/acs.jpcb.1c03380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nucleobase analog 6-thioguanine (6-TG) has emerged as important immunosuppressant, anti-inflammatory, and anticancer drug in the past few decades, but its unique photosensitivity of absorbing strongly ultraviolet UVA light elicits photochemical hazards in many ways. The particularly intriguing yet unresolved question is whether the direct photoreaction of 6-TG can promote DNA-protein cross-links (DPCs) formation, which are large DNA adducts blocking DNA replication and physically impede DNA-related processes. Herein, by real-time observation of radical intermediates using time-resolved UV-vis absorption spectroscopy in conjunction with product analysis by HPLC-MS, we discover that UVA excitation of 6-TG triggers direct covalent cross-linking with tryptophan (TrpH) via an exquisite radical mechanism of electron transfer. The photoexcitation prepares the redox-active triplet 36-TG*, which initiates electron transfer with TrpH, creating TrpH•+ and 6-TG•- in the first step. The deprotonated Trp• undergoes radical-recombination with its geminate partner 6-TG•- and eliminates a H2S, leading to the cross-linking product 6-TG-Trp. The photoadduct structures (two chiral isomers and one constitutional isomer) are identified unambiguously, validating further the mechanism. These findings pinpoint the exact amino acid that is vulnerable to photo-cross-linking with 6-TG and establish a mechanistic framework for understanding mutagenic DPCs formation and developing photoprobes based on this new type of photo-cross-linking.
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Affiliation(s)
- Junjie Dong
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Chunhua Huang
- State Key Lab of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, P. R. China
| | - Shaoshi Guo
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ye Xia
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yue Hou
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xianwang Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ben-Zhan Zhu
- State Key Lab of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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14
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Soszynska-Jozwiak M, Pszczola M, Piasecka J, Peterson JM, Moss WN, Taras-Goslinska K, Kierzek R, Kierzek E. Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus-application of 4-thiouridine photocrosslinking. J Biol Chem 2021; 297:101245. [PMID: 34688660 PMCID: PMC8666676 DOI: 10.1016/j.jbc.2021.101245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/24/2022] Open
Abstract
RNA structure in the influenza A virus (IAV) has been the focus of several studies that have shown connections between conserved secondary structure motifs and their biological function in the virus replication cycle. Questions have arisen on how to best recognize and understand the pandemic properties of IAV strains from an RNA perspective, but determination of the RNA secondary structure has been challenging. Herein, we used chemical mapping to determine the secondary structure of segment 8 viral RNA (vRNA) of the pandemic A/California/04/2009 (H1N1) strain of IAV. Additionally, this long, naturally occurring RNA served as a model to evaluate RNA mapping with 4-thiouridine (4sU) crosslinking. We explored 4-thiouridine as a probe of nucleotides in close proximity, through its incorporation into newly transcribed RNA and subsequent photoactivation. RNA secondary structural features both universal to type A strains and unique to the A/California/04/2009 (H1N1) strain were recognized. 4sU mapping confirmed and facilitated RNA structure prediction, according to several rules: 4sU photocross-linking forms efficiently in the double-stranded region of RNA with some flexibility, in the ends of helices, and across bulges and loops when their structural mobility is permitted. This method highlighted three-dimensional properties of segment 8 vRNA secondary structure motifs and allowed to propose several long-range three-dimensional interactions. 4sU mapping combined with chemical mapping and bioinformatic analysis could be used to enhance the RNA structure determination as well as recognition of target regions for antisense strategies or viral RNA detection.
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Affiliation(s)
| | - Maciej Pszczola
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Julita Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | | | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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15
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Baptista MS, Cadet J, Greer A, Thomas AH. Photosensitization Reactions of Biomolecules: Definition, Targets and Mechanisms. Photochem Photobiol 2021; 97:1456-1483. [PMID: 34133762 DOI: 10.1111/php.13470] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/13/2021] [Indexed: 02/07/2023]
Abstract
Photosensitization reactions have been demonstrated to be largely responsible for the deleterious biological effects of UV and visible radiation, as well as for the curative actions of photomedicine. A large number of endogenous and exogenous photosensitizers, biological targets and mechanisms have been reported in the past few decades. Evolving from the original definitions of the type I and type II photosensitized oxidations, we now provide physicochemical frameworks, classifications and key examples of these mechanisms in order to organize, interpret and understand the vast information available in the literature and the new reports, which are in vigorous growth. This review surveys in an extended manner all identified photosensitization mechanisms of the major biomolecule groups such as nucleic acids, proteins, lipids bridging the gap with the subsequent biological processes. Also described are the effects of photosensitization in cells in which UVA and UVB irradiation triggers enzyme activation with the subsequent delayed generation of superoxide anion radical and nitric oxide. Definitions of photosensitized reactions are identified in biomolecules with key insights into cells and tissues.
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Affiliation(s)
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, Brooklyn, NY, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Andrés H Thomas
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CCT La Plata-CONICET, La Plata, Argentina
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16
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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17
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Mohamadzade A, Ullrich S. Internal conversion and intersystem crossing dynamics of uracil upon double thionation: a time-resolved photoelectron spectroscopy study in the gas phase. Phys Chem Chem Phys 2020; 22:15608-15615. [PMID: 32613978 DOI: 10.1039/d0cp02145h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photophysical properties of 2,4-dithiouracil (2,4-DTU) in the gas phase are studied by time-resolved photoelectron spectroscopy (TRPES) with three different excitation wavelengths in direct extension of previous work on uracil (U), 2-thiouracil (2-TU) and 4-thiouracil (4-TU). Non-radiative deactivation in the canonical nucleobases like uracil mainly occurs via internal conversion (IC) along singlet excited states, although intersystem crossing (ISC) to a long-lived triplet state was confirmed to play a minor role. In thionated uracils, ISC to the triplet state becomes ultrafast and highly efficient with a quantum yield near unity; however, the lifetime of the triplet state is strongly dependent on the position of the sulfur atom. In 2-TU, ISC back to the ground state occurs within a few hundred picoseconds, whereas the population remains trapped in the lowest triplet state in the case of 4-TU. Upon doubling the degree of thionation, ISC remains highly efficient and dominates the photophysics of 2,4-DTU. However, several low-lying excited states contribute to competing IC and ISC pathways and a complex deactivation mechanism, which is evaluated here based on TRPES measurements and discussed in the context of the singly thionated uracils.
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Affiliation(s)
- Abed Mohamadzade
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
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18
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Detection of the thietane precursor in the UVA formation of the DNA 6-4 photoadduct. Nat Commun 2020; 11:3599. [PMID: 32680990 PMCID: PMC7368040 DOI: 10.1038/s41467-020-17333-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
Notwithstanding the central biological role of the (6-4) photoadduct in the induction of skin cancer by sunlight, crucial mechanistic details about its formation have evaded characterization despite efforts spanning more than half a century. 4-Thiothymidine (4tT) has been widely used as an important model system to study its mechanism of formation, but the excited-state precursor, the intermediate species, and the time scale leading to the formation of the (6-4) photoadduct have remained elusive. Herein, steady-state and time-resolved spectroscopic techniques are combined with new and reported quantum-chemical calculations to demonstrate the excited state leading to the formation of the thietane intermediate, its rate, and the formation of the (6-4) photoadduct using the 5’-TT(4tT)T(4tT)TT-3’ DNA oligonucleotide. Efficient, sub-1 ps intersystem crossing leads to the population of a triplet minimum of the thietane intermediate in as short as 3 ps, which intersystem crosses to its ground state and rearranges to form the (6-4) photoadduct. The mechanisms of formation of the (6-4) photoproducts in DNA damage by sunlight is still debated. Here the authors show, by optical spectroscopies and computations, the details of the formation of a (6-4) photoadduct via the thietane intermediate in a single-stranded DNA oligonucleotide.
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19
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Peng Q, Zhu YH, Zhang TS, Liu XY, Fang WH, Cui G. Selenium substitution effects on excited-state properties and photophysics of uracil: a MS-CASPT2 study. Phys Chem Chem Phys 2020; 22:12120-12128. [PMID: 32440669 DOI: 10.1039/d0cp01369b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photophysics of selenium-substituted nucleobases has attracted recent experimental attention because they could serve as potential photosensitizers in photodynamic therapy. Herein, we present a comprehensive MS-CASPT2 study on the spectroscopic and excited-state properties, and photophysics of 2-selenouracil (2SeU), 4-selenouracil (4SeU), and 2,4-selenouracil (24SeU). Relevant minima, conical intersections, crossing points, and excited-state relaxation paths in the lowest five electronic states (i.e., S0, S1, S2, T2, and T1) are explored. On the basis of these results, their photophysical mechanisms are proposed. Upon photoirradiation to the bright S2 state, 2SeU quickly relaxes to its S2 minimum and then moves in an essentially barrierless way to a nearby S2/S1 conical intersection near which the S1 state is populated. Next, the S1 system arrives at an S1/T2/T1 intersection where a large S1/T1 spin-orbit coupling of 430.8 cm-1 makes the T1 state populated. In this state, a barrier of 6.8 kcal mol-1 will trap 2SeU for a while. In parallel, for 4SeU or 24SeU, the system first relaxes to the S2 minimum and then overcomes a small barrier to approach an S2/S1 conical intersection. Once hopping to the S1 state, there exists an extended region with very close S1, T2, and T1 energies. Similarly, a large S1/T1 spin-orbit coupling of 426.8 cm-1 drives the S1→ T1 intersystem crossing process thereby making the T1 state populated. Similarly, an energy barrier heavily suppresses electronic transition to the S0 state. The present work manifests that different selenium substitutions on uracil can lead to a certain extent of different vertical and adiabatic excitation energies, excited-state properties, and relaxation pathways. These insights could help understand the photophysics of selenium-substituted nucleobases.
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Affiliation(s)
- Qin Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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20
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Cao J, Chen DC. The excited-state relaxation mechanism of potential UVA-activated phototherapeutic molecules: trajectory surface hopping simulations of both 4-thiothymine and 2,4-dithiothymine. Phys Chem Chem Phys 2020; 22:10924-10933. [PMID: 32373808 DOI: 10.1039/d0cp01450h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent experimental investigations of the photochemical properties of a series of sulfur-substituted pyrimidine derivatives provide insights into the phototherapeutic potential of these nucleobase variants. Herein we elucidate the triplet formation mechanism of two prospective UVA-activated phototherapeutic molecules, 4-thiothymine and 2,4-dithiothymine, upon photo-excitation by applying the trajectory surface hopping dynamics at the LR-TDDFT level. Our simulations reasonably reproduce the experimental time constants and demonstrate the preferred triplet formation pathway which starts from the S1(nSπ*) state for both molecules. It is found that deactivation of the first bright state to the S1(nSπ*) state proceeds through a mechanism involving elongation of the C5-C6 and C4-S8 bond-lengths and C2-pyramidalization in 4-thiothymine and involving elongation of the C5-C6 and C2-S7 bond-lengths in 2,4-dithiothymine. The intersystem crossing of 2,4-dithiothymine occurs either at geometries characterized by elongated C5-C6 and C2-S7 bond-lengths or at geometries showing elongated C5-C6 and C4-S8 bond-lengths as seen in 4-thiothymine. The solvents are found to affect the S2 state decay of 4-thiothymine, leading to a competing pathway between S2→ S1 and S2→ T3. This study provides a molecular-level understanding of the underlying excited-state relaxation of the two UVA-activated thiopyrimidines, which may be linked to their potential applications in pharmacological science and also prove helpful for designing more effective phototherapeutic agents.
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Affiliation(s)
- Jun Cao
- School of Materials Science and Energy Engineering, Foshan University, Foshan, Guangdong 528000, P. R. China.
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21
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Zhou Y, Routh A. Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. Nucleic Acids Res 2020; 48:e12. [PMID: 31799606 PMCID: PMC6954446 DOI: 10.1093/nar/gkz1124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/31/2019] [Accepted: 11/16/2019] [Indexed: 01/24/2023] Open
Abstract
To characterize RNA-capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: viral Photo-Activatable Ribonucleoside CrossLinking (vPAR-CL). In vPAR-CL, 4-thiouridine is incorporated into the encapsidated genomes of virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that vPAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant vPAR-CL signals across virus RNA genome, indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites coincide with previously identified functional RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining vPAR-CL and DMS-MaPseq reveals that the predominant RNA-capsid interaction sites favored double-stranded RNA regions. We disrupted secondary structures associated with vPAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA-capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- To whom correspondence should be address. Tel: +1 409 772 3663;
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22
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Akkipeddi SMK, Velleca AJ, Carone DM. Probing the function of long noncoding RNAs in the nucleus. Chromosome Res 2020; 28:87-110. [PMID: 32026224 PMCID: PMC7131881 DOI: 10.1007/s10577-019-09625-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 12/29/2019] [Indexed: 12/26/2022]
Abstract
The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other RNA molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncRNAs, along with the ways in which those techniques have revealed insights into their mechanisms of action. Foundational observations into lncRNA function have been gleaned from molecular cytology-based, single-cell approaches to illuminate both the localization and abundance of lncRNAs in addition to their potential binding partners. Biochemical, extraction-based approaches have revealed the molecular contacts between lncRNAs and other molecules within the nuclear environment and how those interactions may contribute to nuclear organization and regulation. Using examples of well-studied nuclear lncRNAs, we demonstrate that the emerging functions of individual lncRNAs have been most clearly deduced from combined cytology and biochemical approaches tailored to study specific lncRNAs. As more functional nuclear lncRNAs continue to emerge, the development of additional technologies to study their interactions and mechanisms of action promise to continually expand our understanding of nuclear organization, chromosome architecture, genome regulation, and disease states.
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Affiliation(s)
| | - Anthony J Velleca
- Department of Molecular Phamacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA, USA.
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23
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Brister MM, Gustavsson T, Crespo-Hernández CE. Excited State Lifetimes of Sulfur-Substituted DNA and RNA Monomers Probed Using the Femtosecond Fluorescence Up-Conversion Technique. Molecules 2020; 25:E584. [PMID: 32013184 PMCID: PMC7037914 DOI: 10.3390/molecules25030584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 11/16/2022] Open
Abstract
Sulfur-substituted DNA and RNA nucleobase derivatives (a.k.a., thiobases) are an important family of biomolecules. They are used as prodrugs and as chemotherapeutic agents in medical settings, and as photocrosslinker molecules in structural-biology applications. Remarkably, excitation of thiobases with ultraviolet to near-visible light results in the population of long-lived and reactive triplet states on a time scale of hundreds of femtoseconds and with near-unity yields. This efficient nonradiative decay pathway explains the vanishingly small fluorescence yields reported for the thiobases and the scarcity of fluorescence lifetimes in the literature. In this study, we report fluorescence lifetimes for twelve thiobase derivatives, both in aqueous solution at physiological pH and in acetonitrile. Excitation is performed at 267 and 362 nm, while fluorescence emission is detected at 380, 425, 450, 525, or 532 nm. All the investigated thiobases reveal fluorescence lifetimes that decay in a few hundreds of femtoseconds and with magnitudes that depend and are sensitive to the position and degree of sulfur-atom substitution and on the solvent environment. Interestingly, however, three thiopyrimidine derivatives (i.e., 2-thiocytidine, 2-thiouridine, and 4-thiothymidine) also exhibit a small amplitude fluorescence component of a few picoseconds in aqueous solution. Furthermore, the N-glycosylation of thiobases to form DNA or RNA nucleoside analogues is demonstrated as affecting their fluorescence lifetimes. In aqueous solution, the fluorescence decay signals exciting at 267 nm are equal or slower than those collected exciting at 362 nm. In acetonitrile, however, the fluorescence decay signals recorded upon 267 nm excitation are, in all cases, faster than those measured exciting at 362 nm. A comparison to the literature values show that, while both the DNA and RNA nucleobase and thiobase derivatives exhibit sub-picosecond fluorescence lifetimes, the 1ππ* excited-state population in the nucleobase monomers primarily decay back to the ground state, whereas it predominantly populates long-lived and reactive triplet states in thiobase monomers.
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Affiliation(s)
- Matthew M. Brister
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA;
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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24
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Skotnicki K, Taras-Goslinska K, Janik I, Bobrowski K. Radiation Induced One-Electron Oxidation of 2-Thiouracil in Aqueous Solutions. Molecules 2019; 24:E4402. [PMID: 31810289 PMCID: PMC6930642 DOI: 10.3390/molecules24234402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 11/17/2022] Open
Abstract
Oxidative damage to 2-thiouracil (2-TU) by hydroxyl (•OH) and azide (●N3) radicals produces various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by time-dependent density functional theory (TD-DFT) method. The transient absorption spectra recorded in the reactions of •OH with 2-TU depend on the concentration of 2-TU, however, only slightly on pH. At low concentrations, they are characterized by a broad absorption band with a weakly pronounced maxima located at λ = 325, 340 and 385 nm, whereas for high concentrations, they are dominated by an absorption band with λmax ≈ 425 nm. Based on calculations using TD-DFT method, the transient absorption spectra at low concentration of 2-TU were assigned to the ●OH-adducts to the double bond at C5 and C6 carbon atoms (3●, 4●) and 2c-3e bonded ●OH adduct to sulfur atom (1…●OH) and at high concentration of 2-TU also to the dimeric 2c-3e S-S-bonded radical in neutral form (2●). The dimeric radical (2●) is formed in the reaction of thiyl-type radical (6●) with 2-TU and both radicals are in an equilibrium with Keq = 4.2 × 103 M-1. Similar equilibrium (with Keq = 4.3 × 103 M-1) was found for pH above the pKa of 2-TU which involves admittedly the same radical (6●) but with the dimeric 2c-3e S-S bonded radical in anionic form (2●-). In turn, ●N3-induced oxidation of 2-TU occurs via radical cation with maximum spin location on the sulfur atom which subsequently undergoes deprotonation at N1 atom leading again to thiyl-type radical (6●). This radical is a direct precursor of dimeric radical (2●).
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Affiliation(s)
- Konrad Skotnicki
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | | | - Ireneusz Janik
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
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25
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Yermolina MV, Papadantonakis GA. Electron and radical cation of sulfur-substituted thymine derivatives produced near photoionization threshold can alter and distort double-helix DNA structure. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Abe YS, Sasaki S. The adduct formation between the thioguanine-polyamine ligands and DNA with the AP site under UVA irradiated and non-irradiated conditions. Bioorg Med Chem 2019; 27:115160. [PMID: 31706680 DOI: 10.1016/j.bmc.2019.115160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022]
Abstract
The AP sites are representative of DNA damage and known as an intermediate in the base excision repair (BER) pathway which is involved in the repair of damaged nucleobases by reactive oxygen species, UVA irradiation, and DNA alkylating agents. Therefore, it is expected that the inhibition or modulation of the AP site repair pathway may be a new type of anticancer drug. In this study, we investigated the effects of the thioguanine-polyamine ligands (SG-ligands) on the affinity and the reactivity for the AP site under UVA irradiated and non-irradiated conditions. The SG-ligands have a photo-reactivity with the A-F-C sequence where F represents a tetrahydrofuran AP site analogue. Interestingly, the SG-ligands promoted the β-elimination of the AP site followed by the formation of a covalent bond with the β-eliminated fragment without UVA irradiation.
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Affiliation(s)
- Yukiko S Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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27
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Taras-Goslinska K, Vetica F, Barata-Vallejo S, Triantakostanti V, Marciniak B, Chatgilialoglu C. Converging Fate of the Oxidation and Reduction of 8-Thioguanosine. Molecules 2019; 24:E3143. [PMID: 31470553 PMCID: PMC6749358 DOI: 10.3390/molecules24173143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022] Open
Abstract
Thione-containing nucleobases have attracted the attention of the scientific community for their application in oncology, virology, and transplantology. The detailed understanding of the reactivity of the purine derivative 8-thioguanosine (8-TG) with reactive oxygen species (ROS) and free radicals is crucial for its biological relevance. An extensive investigation on the fate of 8-TG under both reductive and oxidative conditions is here reported, and it was tested by employing steady-state photooxidation, laser flash photolysis, as well as γ-radiolysis in aqueous solutions. The characterization of the 8-TG T1 excited state by laser flash photolysis and the photooxidation experiments confirmed that singlet oxygen is a crucial intermediate in the formation of the unexpected reduced product guanosine, without the formation of the usual oxygenated sulfinic or sulfonic acids. Furthermore, a thorough screening of different radiolytic conditions upon γ-radiation afforded the reduced product. These results were rationalized by performing control experiments in the predominant presence of each reactive species formed by radiolysis of water, and the mechanistic pathway scenario was postulated on these bases.
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Affiliation(s)
| | - Fabrizio Vetica
- R&D Laboratory, Lipinutragen srl, Via Piero Gobetti 101, 40129 Bologna, Italy
- ISOF, Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
| | - Sebastián Barata-Vallejo
- ISOF, Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimíca, Departamento de Quimíca Organíca, Junin 954, RA-1113 Buenos Aires, Argentina
| | | | - Bronisław Marciniak
- Adam Mickiewicz University, Faculty of Chemistry, Wieniawskiego 1, 61-712 Poznań, Poland
- Center of Advanced Technologies, Adam Mickiewicz University, 61-712 Poznań, Poland
| | - Chryssostomos Chatgilialoglu
- R&D Laboratory, Lipinutragen srl, Via Piero Gobetti 101, 40129 Bologna, Italy.
- ISOF, Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy.
- Center of Advanced Technologies, Adam Mickiewicz University, 61-712 Poznań, Poland.
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28
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Onizuka K, Ishida K, Mano E, Nagatsugi F. Alkyne-Alkyne Photo-cross-linking on the Flipping-out Field. Org Lett 2019; 21:2833-2837. [PMID: 30951316 DOI: 10.1021/acs.orglett.9b00817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base flip-inducing nucleic acids are expected to create a specific field for various chemical reactions. We now report a novel type of base-flip-inducing oligodeoxynucleotide and photo-cross-linking reaction. Two 3-arylethynyl-5-methyl-2-pyridone nucleosides, Ph and An, were synthesized, and their properties were investigated. The alkyne-alkyne photo-cross-linking rapidly proceeded by taking advantage of the base-flipping-out field where two alkynes overlap each other. This photo-cross-linking would be a new candidate to form cross-linked DNAs.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Kei Ishida
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
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29
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Gładysz M, Andrałojć W, Czapik T, Gdaniec Z, Kierzek R. Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA. Sci Rep 2019; 9:4385. [PMID: 30867505 PMCID: PMC6416399 DOI: 10.1038/s41598-019-40715-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/21/2019] [Indexed: 12/21/2022] Open
Abstract
Thionucleotides, especially 4-thiouridine and 6-thioguanosine, are photosensitive molecules that photocrosslink to both proteins and nucleic acids, and this feature is a major reason for their application in various investigations. To get insight into the thermodynamic and structural contributions of 6-thioguanosine to the properties of RNA duplexes a systematic study was performed. In a series of RNA duplexes, selected guanosine residues located in G-C base pairs, mismatches (G-G, G-U, and G-A), or 5' and 3'-dangling ends were replaced with 6-thioguanosine. Generally, the presence of 6-thioguanosine diminishes the thermodynamic stability of RNA duplexes. This effect depends on its position within duplexes and the sequence of adjacent base pairs. However, when placed at a dangling end a 6-thioguanosine residue actually exerts a weak stabilizing effect. Furthermore, the structural effect of 6-thioguanosine substitution appears to be minimal based on NMR and Circular Dichroism (CD) data.
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Affiliation(s)
- Michał Gładysz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Tomasz Czapik
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland.
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30
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Di Mascio P, Martinez GR, Miyamoto S, Ronsein GE, Medeiros MHG, Cadet J. Singlet Molecular Oxygen Reactions with Nucleic Acids, Lipids, and Proteins. Chem Rev 2019; 119:2043-2086. [DOI: 10.1021/acs.chemrev.8b00554] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Glaucia R. Martinez
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, 81531-990 Curitiba, PR, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Graziella E. Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Marisa H. G. Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4 Québec, Canada
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31
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Zou X, Sun Z, Zhao H, Zhang CY. Mechanistic insight into photocrosslinking reaction between triplet state 4-thiopyrimidine and thymine. Phys Chem Chem Phys 2019; 21:21305-21316. [DOI: 10.1039/c9cp04089g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple nonadiabatic pathways greatly facilitate the proceeding of photocrosslinking reactions between 4-thiopyrimidine and thymine.
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Affiliation(s)
- Xiaoran Zou
- 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
| | - Zhonghua 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
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Science
- Beijing
- P. R. China
| | - Chun-yang Zhang
- 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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32
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Ashwood B, Pollum M, Crespo-Hernández CE. Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases. Photochem Photobiol 2018; 95:33-58. [PMID: 29978490 DOI: 10.1111/php.12975] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/28/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Case Western Reserve University, Cleveland, OH
| | - Marvin Pollum
- Department of Chemistry, Case Western Reserve University, Cleveland, OH
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33
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Gérard-Hirne T, Thiebaut F, Sachon E, Désert A, Drujon T, Guérineau V, Michel BY, Benhida R, Coulon S, Saintomé C, Guianvarc'h D. Photoactivatable oligonucleotide probes to trap single-stranded DNA binding proteins: Updating the potential of 4-thiothymidine from a comparative study. Biochimie 2018; 154:164-175. [PMID: 30171884 DOI: 10.1016/j.biochi.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023]
Abstract
Photoaffinity labeling (PAL) in combination with recent developments in mass spectrometry is a powerful tool for studying nucleic acid-protein interactions, enabling crosslinking of both partners through covalent bond formation. Such a strategy requires a preliminary study of the most judicious photoreactive group to crosslink efficiently with the target protein. In this study, we report a survey of three different photoreactive nucleobases (including a guanine functionalized with a benzophenone or a diazirine and the zero-length agent 4-thiothymine) incorporated in 30-mer oligonucleotides (ODN) containing a biotin moiety for selective trapping and enrichment of single-stranded DNA binding proteins (SSB). First, the conditions and efficiency of the photochemical reaction with a purified protein using human replication protein A as the relevant model was studied. Secondly, the ability of the probe as bait to photocrosslink and enrich SSB in cell lysate was addressed. Among the different ODN probes studied, we showed that 4-thiothymine was the most relevant: i) it allows efficient and specific trapping of SSB in whole cell extracts in a similar extent as the widely used diazirine, ii) it features the advantages of a zero-length agent thus retaining the physicochemical properties of the ODN bait; iii) ODN including this photochemical agent are easily accessible. In combination with mass spectrometry, the probes incorporating this nucleobase are powerful tools for PAL strategies and can be added in the toolbox of the traditional photocrosslinkers for studying DNA-protein interactions.
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Affiliation(s)
- Tom Gérard-Hirne
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Frédéric Thiebaut
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; MNHN CNRS UMR 7196, INSERM U1154, 43 Rue Cuvier, 75005, Paris, France
| | - Emmanuelle Sachon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; Plateforme de spectrométrie de masse et protéomique, IBPS, FR3631, UPMC, 4 Place Jussieu, 75005, Paris, France
| | - Alexandre Désert
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Thierry Drujon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Benoît Y Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France
| | - Stéphane Coulon
- CRCM, CNRS, Inserm, Aix-Marseille Univ, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Carole Saintomé
- MNHN CNRS UMR 7196, INSERM U1154, 43 Rue Cuvier, 75005, Paris, France; Sorbonne Université, UFR927, 4, Place Jussieu, F-75005, Paris, France.
| | - Dominique Guianvarc'h
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; Institut de Chimie Moléculaire et des Matériaux d'Orsay, Univ. Paris-Sud, CNRS, Université Paris-Saclay, F-91405, Orsay, France.
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34
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Farrell KM, Brister MM, Pittelkow M, Sølling TI, Crespo-Hernández CE. Heavy-Atom-Substituted Nucleobases in Photodynamic Applications: Substitution of Sulfur with Selenium in 6-Thioguanine Induces a Remarkable Increase in the Rate of Triplet Decay in 6-Selenoguanine. J Am Chem Soc 2018; 140:11214-11218. [DOI: 10.1021/jacs.8b07665] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Kieran M. Farrell
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Matthew M. Brister
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Theis I. Sølling
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Carlos E. Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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35
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Pollum M, Lam M, Jockusch S, Crespo‐Hernández CE. Dithionated Nucleobases as Effective Photodynamic Agents against Human Epidermoid Carcinoma Cells. ChemMedChem 2018. [DOI: 10.1002/cmdc.201800148] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Marvin Pollum
- Department of Chemistry Case Western Reserve University Cleveland OH 44106 USA
| | - Minh Lam
- Department of Medicine Case Western Reserve University School of Medicine Cleveland OH 44106 USA
| | - Steffen Jockusch
- Department of Chemistry Columbia University New York NY 10027 USA
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36
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Galej WP, Toor N, Newman AJ, Nagai K. Molecular Mechanism and Evolution of Nuclear Pre-mRNA and Group II Intron Splicing: Insights from Cryo-Electron Microscopy Structures. Chem Rev 2018; 118:4156-4176. [PMID: 29377672 DOI: 10.1021/acs.chemrev.7b00499] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor. Prp8, the largest and most conserved protein in the spliceosome, cradles the active site RNA. Prp8 and group II intron maturase have a similar domain architecture, suggesting that they also share a common evolutionary origin. The interactions between maturase and key group II intron RNA elements, such as the exon-binding loop and domains V and VI, are recapitulated in the interactions between Prp8 and key elements in the spliceosome's catalytic RNA core. Structural comparisons suggest that the extensive RNA scaffold of the group II intron was gradually replaced by proteins as the spliceosome evolved. A plausible model of spliceosome evolution is discussed.
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Affiliation(s)
- Wojciech P Galej
- EMBL Grenoble , 71 Avenue des Martyrs , 38042 Grenoble Cedex 09 , France
| | - Navtej Toor
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , U.K
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37
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Warneford-Thomson R, He C, Sidoli S, Garcia BA, Bonasio R. Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions. J Vis Exp 2017. [PMID: 28994809 DOI: 10.3791/56004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most cases, the action of noncoding RNAs is mediated by proteins whose functions are in turn regulated by these interactions with noncoding RNAs. Consistent with this, a growing number of proteins involved in nuclear functions have been reported to bind RNA and in a few cases the RNA-binding regions of these proteins have been mapped, often through laborious, candidate-based methods. Here, we report a detailed protocol to perform a high-throughput, proteome-wide unbiased identification of RNA-binding proteins and their RNA-binding regions. The methodology relies on the incorporation of a photoreactive uridine analog in the cellular RNA, followed by UV-mediated protein-RNA crosslinking, and mass spectrometry analyses to reveal RNA-crosslinked peptides within the proteome. Although we describe the procedure for mouse embryonic stem cells, the protocol should be easily adapted to a variety of cultured cells.
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Affiliation(s)
- Robert Warneford-Thomson
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine; Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine
| | - Chongsheng He
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine
| | - Simone Sidoli
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine; Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine
| | - Benjamin A Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine; Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine;
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38
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Arslancan S, Martínez-Fernández L, Corral I. Photophysics and Photochemistry of Canonical Nucleobases’ Thioanalogs: From Quantum Mechanical Studies to Time Resolved Experiments. Molecules 2017. [PMCID: PMC6152766 DOI: 10.3390/molecules22060998] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Interest in understanding the photophysics and photochemistry of thiated nucleobases has been awakened because of their possible involvement in primordial RNA or their potential use as photosensitizers in medicinal chemistry. The interpretation of the photodynamics of these systems, conditioned by their intricate potential energy surfaces, requires the powerful interplay between experimental measurements and state of the art molecular simulations. In this review, we provide an overview on the photophysics of natural nucleobases’ thioanalogs, which covers the last 30 years and both experimental and computational contributions. For all the canonical nucleobase’s thioanalogs, we have compiled the main steady state absorption and emission features and their interpretation in terms of theoretical calculations. Then, we revise the main topographical features, including stationary points and interstate crossings, of their potential energy surfaces based on quantum mechanical calculations and we conclude, by combining the outcome of different spectroscopic techniques and molecular dynamics simulations, with the mechanism by which these nucleobase analogs populate their triplet excited states, which are at the origin of their photosensitizing properties.
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Affiliation(s)
- Serra Arslancan
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain;
| | - Lara Martínez-Fernández
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, Napoli I-80134, Italy
- Correspondence: (L.M.-F.); (I.C.); Tel.: +34-91-497-8471 (I.C.)
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain;
- Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Correspondence: (L.M.-F.); (I.C.); Tel.: +34-91-497-8471 (I.C.)
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39
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Chang XP, Xiao P, Han J, Fang WH, Cui G. A theoretical study of the light-induced cross-linking reaction of 5-fluoro-4-thiouridine with thymine. Phys Chem Chem Phys 2017; 19:13524-13533. [PMID: 28498381 DOI: 10.1039/c7cp01511a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In contrast to photophysics of thio-substituted nucleobases, their photoinduced cross-linking reactions with canonical nucleobases remain scarcely investigated computationally. In this work, we have adopted combined CASPT2/PCM//CASSCF and B3LYP-D3/PCM electronic structure methods to study this kind of photochemical reaction of 5-fluoro-4-thiouridine (truncated 5-fluoro-1-methyl-4-thiouracil used in calculations) and 1-methylthymine (referred to as thymine for clarity hereinafter). On the basis of CASPT2/PCM computed results, we have proposed two efficient excited-state relaxation pathways to populate the lowest T1 state of the complex of 5-fluoro-1-methyl-4-thiouracil and thymine from its initially populated S2(1ππ*) state. In the first one, the S2 system first hops to the S1 state via an S2/S1 conical intersection, followed by a direct S1 → T1 intersystem crossing process enhanced by large S1/T1 spin-orbit coupling. In the second path, the resultant S1 system first jumps to the T2 state, from which an efficient T2 → T1 internal conversion occurs. The T1 cross-linking reaction is overall divided into two phases. The first phase is a stepwise and nonadiabatic photocyclization reaction, which starts from the T1 complex and ends up with an S0 thietane intermediate. The second phase is a thermal reaction. The system first rearranges its four- and six-membered rings to form three new rings; then, an S0 fluorine atom transfer occurs, followed by the formation of photoproducts. Finally, the present work paves the way for studying light-induced cross-linking reactions of thionucleobases with canonical bases in DNA and RNA.
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Affiliation(s)
- Xue-Ping Chang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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40
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Mai S, Ashwood B, Marquetand P, Crespo-Hernández CE, González L. Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine. J Phys Chem B 2017; 121:5187-5196. [PMID: 28452483 PMCID: PMC5447245 DOI: 10.1021/acs.jpcb.7b02715] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Indexed: 01/01/2023]
Abstract
The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents.
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Affiliation(s)
- Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Brennan Ashwood
- Center
for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Carlos E. Crespo-Hernández
- Center
for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
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41
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Tauraitė D, Jakubovska J, Dabužinskaitė J, Bratchikov M, Meškys R. Modified Nucleotides as Substrates of Terminal Deoxynucleotidyl Transferase. Molecules 2017; 22:molecules22040672. [PMID: 28441732 PMCID: PMC6154577 DOI: 10.3390/molecules22040672] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/10/2017] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
The synthesis of novel modified nucleotides and their incorporation into DNA sequences opens many possibilities to change the chemical properties of oligonucleotides (ONs), and, therefore, broaden the field of practical applications of modified DNA. The chemical synthesis of nucleotide derivatives, including ones bearing thio-, hydrazino-, cyano- and carboxy groups as well as 2-pyridone nucleobase-containing nucleotides was carried out. The prepared compounds were tested as substrates of terminal deoxynucleotidyl transferase (TdT). The nucleotides containing N4-aminocytosine, 4-thiouracil as well as 2-pyridone, 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by TdT, thus allowing enzymatic synthesis of 3’-terminally modified ONs. The successful UV-induced cross-linking of 4-thiouracil-containing ONs to TdT was carried out. Enzymatic post-synthetic 3’-modification of ONs with various photo- and chemically-reactive groups opens novel possibilities for future applications, especially in analysis of the mechanisms of polymerases and the development of photo-labels, sensors, and self-assembling structures.
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Affiliation(s)
- Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Julija Dabužinskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Maksim Bratchikov
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio g. 21, Vilnius LT-03101, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
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42
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Martínez-Fernández L, Granucci G, Pollum M, Crespo-Hernández CE, Persico M, Corral I. Decoding the Molecular Basis for the Population Mechanism of the Triplet Phototoxic Precursors in UVA Light-Activated Pyrimidine Anticancer Drugs. Chemistry 2017; 23:2619-2627. [DOI: 10.1002/chem.201604543] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química; Universidad Autónoma de Madrid; 28049 Cantoblanco, Madrid Spain
- Current address: Istituto di Biostrutture e Bioimmagini; Consiglio delle Ricerche; 80134 Napoli Italy
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; v. G. Moruzzi 3 56124 Pisa Italy
| | - Marvin Pollum
- Department of Chemistry and Center for Chemical Dynamics; Case Western Reserve University; 10900 Euclid Avenue Cleveland OH 44106 USA
| | - Carlos E. Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics; Case Western Reserve University; 10900 Euclid Avenue Cleveland OH 44106 USA
| | - Maurizio Persico
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; v. G. Moruzzi 3 56124 Pisa Italy
| | - Inés Corral
- Departamento de Química; Universidad Autónoma de Madrid; 28049 Cantoblanco, Madrid Spain
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43
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Martinez-Fernandez L, Fahleson T, Norman P, Santoro F, Coriani S, Improta R. Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution. Photochem Photobiol Sci 2017; 16:1415-1423. [DOI: 10.1039/c7pp00105c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.
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Affiliation(s)
| | - T. Fahleson
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - P. Norman
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - F. Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
| | - S. Coriani
- Department of Chemistry
- Technical University of Denmark
- Denmark
| | - R. Improta
- Istituto di Biostrutture e Bioimmagini-CNR
- I-80134 Napoli
- Italy
- LIDYL
- CEA
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44
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Guven M, Barnouin K, Snijders AP, Karran P. Photosensitized UVA-Induced Cross-Linking between Human DNA Repair and Replication Proteins and DNA Revealed by Proteomic Analysis. J Proteome Res 2016; 15:4612-4623. [PMID: 27654267 PMCID: PMC5154610 DOI: 10.1021/acs.jproteome.6b00717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 11/29/2022]
Abstract
Long wavelength ultraviolet radiation (UVA, 320-400 nm) interacts with chromophores present in human cells to induce reactive oxygen species (ROS) that damage both DNA and proteins. ROS levels are amplified, and the damaging effects of UVA are exacerbated if the cells are irradiated in the presence of UVA photosensitizers such as 6-thioguanine (6-TG), a strong UVA chromophore that is extensively incorporated into the DNA of dividing cells, or the fluoroquinolone antibiotic ciprofloxacin. Both DNA-embedded 6-TG and ciprofloxacin combine synergistically with UVA to generate high levels of ROS. Importantly, the extensive protein damage induced by these photosensitizer+UVA combinations inhibits DNA repair. DNA is maintained in intimate contact with the proteins that effect its replication, transcription, and repair, and DNA-protein cross-links (DPCs) are a recognized reaction product of ROS. Cross-linking of DNA metabolizing proteins would compromise these processes by introducing physical blocks and by depleting active proteins. We describe a sensitive and statistically rigorous method to analyze DPCs in cultured human cells. Application of this proteomics-based analysis to cells treated with 6-TG+UVA and ciprofloxacin+UVA identified proteins involved in DNA repair, replication, and gene expression among those most vulnerable to cross-linking under oxidative conditions.
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Affiliation(s)
- Melisa Guven
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
| | - Karin Barnouin
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
| | - Ambrosius P. Snijders
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
| | - Peter Karran
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
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45
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Ruckenbauer M, Mai S, Marquetand P, González L. Photoelectron spectra of 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil. J Chem Phys 2016; 144:074303. [PMID: 26896982 DOI: 10.1063/1.4941948] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ground- and excited-state UV photoelectron spectra of thiouracils (2-thiouracil, 4-thiouracil, and 2,4-dithiouracil) have been simulated using multireference configuration interaction calculations and Dyson norms as a measure for the photoionization intensity. Except for a constant shift, the calculated spectrum of 2-thiouracil agrees very well with experiment, while no experimental spectra are available for the two other compounds. For all three molecules, the photoelectron spectra show distinct bands due to ionization of the sulphur and oxygen lone pairs and the pyrimidine π system. The excited-state photoelectron spectra of 2-thiouracil show bands at much lower energies than in the ground state spectrum, allowing to monitor the excited-state population in time-resolved UV photoelectron spectroscopy experiments. However, the results also reveal that single-photon ionization probe schemes alone will not allow monitoring all photodynamic processes existing in 2-thiouracil. Especially, due to overlapping bands of singlet and triplet states the clear observation of intersystem crossing will be hampered.
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Affiliation(s)
- Matthias Ruckenbauer
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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46
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Sigel A, Operschall BP, Matera-Witkiewicz A, Świątek-Kozłowska J, Sigel H. Acid–base and metal ion-binding properties of thiopyrimidine derivatives. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Mai S, Pollum M, Martínez-Fernández L, Dunn N, Marquetand P, Corral I, Crespo-Hernández CE, González L. The origin of efficient triplet state population in sulfur-substituted nucleobases. Nat Commun 2016; 7:13077. [PMID: 27703148 PMCID: PMC5059480 DOI: 10.1038/ncomms13077] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/01/2016] [Indexed: 12/19/2022] Open
Abstract
Elucidating the photophysical mechanisms in sulfur-substituted nucleobases (thiobases) is essential for designing prospective drugs for photo- and chemotherapeutic applications. Although it has long been established that the phototherapeutic activity of thiobases is intimately linked to efficient intersystem crossing into reactive triplet states, the molecular factors underlying this efficiency are poorly understood. Herein we combine femtosecond transient absorption experiments with quantum chemistry and nonadiabatic dynamics simulations to investigate 2-thiocytosine as a necessary step to unravel the electronic and structural elements that lead to ultrafast and near-unity triplet-state population in thiobases in general. We show that different parts of the potential energy surfaces are stabilized to different extents via thionation, quenching the intrinsic photostability of canonical DNA and RNA nucleobases. These findings satisfactorily explain why thiobases exhibit the fastest intersystem crossing lifetimes measured to date among bio-organic molecules and have near-unity triplet yields, whereas the triplet yields of canonical nucleobases are nearly zero.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Marvin Pollum
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | | | - Nicholas Dunn
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Inés Corral
- Universidad Autónoma de Madrid, Departamento de Química, Cantoblanco, Madrid 28049, Spain
| | - Carlos E. Crespo-Hernández
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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48
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Pollum M, Jockusch S, Crespo-Hernández CE. Increase in the photoreactivity of uracil derivatives by doubling thionation. Phys Chem Chem Phys 2016; 17:27851-61. [PMID: 26439833 DOI: 10.1039/c5cp04822b] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability of 4-thiouracil to strongly absorb UVA radiation and to populate a reactive triplet state in high yield has enabled its use as a versatile photocrosslinker for nearly 50 years. In this contribution, we present a detailed spectroscopic and photochemical investigation of the 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil series in an effort to further advance this chemistry and to scrutinize the photoreactivity of 2,4-dithiouracil. Our results reveal that excitation of 2,4-dithiouracil leads to intersystem crossing to the triplet manifold in 220 ± 40 fs, which enables the population of the reactive triplet state with near unity yield (ΦT = 0.90 ± 0.15) and ultimately leads to a ca. 50% singlet oxygen generation (ΦΔ = 0.49 ± 0.02)-one of the highest singlet oxygen yields reported to date for a photoexcited thiobase. In addition, the long-lived triplet state of 2,4-dithiouracil reacts efficiently with the nucleic acid base adenine 5'-monophosphate through a direct, oxygen-independent photocycloaddition mechanism and at a rate that is at least 3-fold faster than that of 4-thiouracil under equal conditions. The new physico-chemical insights reported for these RNA-thiobase derivatives are compared to those of the DNA and RNA bases and the DNA-thiobase derivatives. Furthermore, the strong near-visible absorption and increased photoreactivity measured for 2,4-dithiouracil lays a solid foundation for developing RNA-targeted photocrosslinking and phototherapeutic agents that are more effective than those currently available.
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Affiliation(s)
- M Pollum
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, OH 44106, USA.
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49
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Safa L, Gueddouda NM, Thiébaut F, Delagoutte E, Petruseva I, Lavrik O, Mendoza O, Bourdoncle A, Alberti P, Riou JF, Saintomé C. 5' to 3' Unfolding Directionality of DNA Secondary Structures by Replication Protein A: G-QUADRUPLEXES AND DUPLEXES. J Biol Chem 2016; 291:21246-21256. [PMID: 27440048 DOI: 10.1074/jbc.m115.709667] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 11/06/2022] Open
Abstract
The replication protein A (RPA) is a single-stranded DNA-binding protein that plays an essential role in DNA metabolism. RPA is able to unfold G-quadruplex (G4) structures formed by telomeric DNA sequences, a function important for telomere maintenance. To elucidate the mechanism through which RPA unfolds telomeric G4s, we studied its interaction with oligonucleotides that adopt a G4 structure extended with a single-stranded tail on either side of the G4. Binding and unfolding was characterized using several biochemical and biophysical approaches and in the presence of specific G4 ligands, such as telomestatin and 360A. Our data show that RPA can bind on each side of the G4 but it unwinds the G4 only from 5' toward 3'. We explain the 5' to 3' unfolding directionality in terms of the 5' to 3' oriented laying out of hRPA subunits along single-stranded DNA. Furthermore, we demonstrate by kinetics experiments that RPA proceeds with the same directionality for duplex unfolding.
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Affiliation(s)
- Layal Safa
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France, the Sorbonne Universités, UPMC University Paris 06, F-75005, Paris, France
| | - Nassima Meriem Gueddouda
- the Laboratoire ARNA-INSERM U1212, UMR 5320, Institut européen de chimie et biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Thiébaut
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France, the Sorbonne Universités, UPMC University Paris 06, F-75005, Paris, France, the Ecole Normale Supérieure, PSL Research University, Département de Chimie, 24 rue Lhomond, CNRS, UMR 7203 LBM, 75005 Paris, France, and
| | - Emmanuelle Delagoutte
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France
| | - Irina Petruseva
- the Novosibirsk Institute of Chemical Biology and Fundamental Medecine, Siberian Division of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Olga Lavrik
- the Novosibirsk Institute of Chemical Biology and Fundamental Medecine, Siberian Division of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Oscar Mendoza
- the Laboratoire ARNA-INSERM U1212, UMR 5320, Institut européen de chimie et biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Anne Bourdoncle
- the Laboratoire ARNA-INSERM U1212, UMR 5320, Institut européen de chimie et biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Patrizia Alberti
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France,
| | - Jean-François Riou
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France
| | - Carole Saintomé
- From the Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, CP26, 57 rue Cuvier, 75005, Paris, France, the Sorbonne Universités, UPMC University Paris 06, F-75005, Paris, France,
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50
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Mai S, Marquetand P, González L. Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture. J Phys Chem Lett 2016; 7:1978-83. [PMID: 27167106 PMCID: PMC4893732 DOI: 10.1021/acs.jpclett.6b00616] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The deactivation mechanism after ultraviolet irradiation of 2-thiouracil has been investigated using nonadiabatic dynamics simulations at the MS-CASPT2 level of theory. It is found that after excitation the S2 quickly relaxes to S1, and from there intersystem crossing takes place to both T2 and T1 with a time constant of 400 fs and a triplet yield above 80%, in very good agreement with recent femtosecond experiments in solution. Both indirect S1 → T2 → T1 and direct S1 → T1 pathways contribute to intersystem crossing, with the former being predominant. The results contribute to the understanding of how some noncanonical nucleobases respond to harmful ultraviolet light, which could be relevant for prospective photochemotherapeutic applications.
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