1
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Markovitsi D. Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors. Photochem Photobiol 2024; 100:262-274. [PMID: 37365765 DOI: 10.1111/php.13826] [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: 05/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures exhibiting an important polymorphism. During the past two decades, their study by time-resolved spectroscopy, from femtoseconds to milliseconds, associated to computational methods, shed light on the primary processes occurring when they absorb UV radiation. Quite recently, their utilization in label-free and dye-free biosensors was explored by a few groups. In view of such developments, this review discusses the outcomes of the fundamental studies that could contribute to the design of future optoelectronic biosensors using fluorescence or charge carriers stemming directly from GQs, without mediation of other molecules, as it is the currently the case. It explains how the excited state relaxation influences both the fluorescence intensity and the efficiency of low-energy photoionization, occurring via a complex mechanism. The corresponding quantum yields, determined with excitation at 266/267 nm, fall in the range of (3.0-9.5) × 10-4 and (3.2-9.2) × 10-3 , respectively. These values, significantly higher than the corresponding values found for duplexes, depend strongly on certain structural factors (molecularity, metal cations, peripheral bases, number of tetrads …) which intervene in the relaxation process. Accordingly, these features can be tuned to optimize the desired signal.
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Affiliation(s)
- Dimitra Markovitsi
- CNRS, Institut de Chimie Physique, UMR8000, Université Paris-Saclay, Orsay, France
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2
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Feng Y, Luo Z, Huang R, Yang X, Cheng X, Zhang W. Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2022; 23:ijms23158404. [PMID: 35955535 PMCID: PMC9368837 DOI: 10.3390/ijms23158404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
DNA G-quadruplexes (G4s) are non-canonical four-stranded DNA structures involved in various biological processes in eukaryotes. Molecularly crowded solutions and monovalent cations have been reported to stabilize in vitro and in vivo G4 formation. However, how K+ and Na+ affect G4 formation genome-wide is still unclear in plants. Here, we conducted BG4-DNA-IP-seq, DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing, under K+ and Na+ + PEG conditions in vitro. We found that K+-specific IP-G4s had a longer peak size, more GC and PQS content, and distinct AT and GC skews compared to Na+-specific IP-G4s. Moreover, K+- and Na+-specific IP-G4s exhibited differential subgenomic enrichment and distinct putative functional motifs for the binding of certain trans-factors. More importantly, we found that K+-specific IP-G4s were more associated with active marks, such as active histone marks, and low DNA methylation levels, as compared to Na+-specific IP-G4s; thus, K+-specific IP-G4s in combination with active chromatin features facilitate the expression of overlapping genes. In addition, K+- and Na+-specific IP-G4 overlapping genes exhibited differential GO (gene ontology) terms, suggesting they may have distinct biological relevance in rice. Thus, our study, for the first time, explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Ranran Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Xueming Yang
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
- Correspondence: ; Tel.: +86-25-84396610; Fax: +86-25-84396302
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3
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Milovanović B, Petković M, Etinski M. Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120584. [PMID: 34794899 DOI: 10.1016/j.saa.2021.120584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca2+, Sr2+ and Ba2+). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca2+ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.
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Affiliation(s)
- Branislav Milovanović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Milena Petković
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia.
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4
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Asha H, Stadlbauer P, Martínez-Fernández L, Banáš P, Šponer J, Improta R, Esposito L. Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine. Int J Biol Macromol 2022; 194:882-894. [PMID: 34838862 DOI: 10.1016/j.ijbiomac.2021.11.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022]
Abstract
Guanine radical cation (G•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)3 (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G•+ (Tel21+). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21+ systems, differing in the position of G•+ in the sequence. When G•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na+ ions and increase the solvent exposed surface of G•+. Analysis of solvation patterns of G•+ provides new insights on the main reactions of G•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.
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Affiliation(s)
- Haritha Asha
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lara Martínez-Fernández
- Departamento de Quimica, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autonoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
| | - Luciana Esposito
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
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5
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Balanikas E, Martinez-Fernandez L, Baldacchino G, Markovitsi D. Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups. Int J Mol Sci 2021; 22:ijms222413436. [PMID: 34948235 PMCID: PMC8704496 DOI: 10.3390/ijms222413436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G+)● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.
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Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Lara Martinez-Fernandez
- Departamento de Química, Modúlo 13, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Correspondence: (L.M.-F.); or (D.M.)
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
- Correspondence: (L.M.-F.); or (D.M.)
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6
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Milovanović B, Petković M, Popov I, Etinski M. Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex. J Phys Chem B 2021; 125:11996-12005. [PMID: 34694801 DOI: 10.1021/acs.jpcb.1c05598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.
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Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16 11000 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16 11000 Belgrade, Serbia
| | - Igor Popov
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia.,Institut of Physics, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16 11000 Belgrade, Serbia
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7
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Segarra‐Martí J, Bearpark MJ. Modelling Photoionisation in Isocytosine: Potential Formation of Longer-Lived Excited State Cations in its Keto Form. Chemphyschem 2021; 22:2172-2181. [PMID: 34370368 PMCID: PMC8597144 DOI: 10.1002/cphc.202100402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/09/2021] [Indexed: 11/24/2022]
Abstract
Studying the effects of UV and VUV radiation on non-canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS-CASPT2 theoretical study of the photoionisation of non-canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2 π + , 2 n O + and 2 n N + and compare these to the corresponding electronic states in cytosine. Investigating lower-energy decay pathways we find - unexpectedly - that keto-isocytosine+ presents a sizeable energy barrier potentially inhibiting decay to its cationic ground state, whereas enol-isocytosine+ features a barrierless and consequently ultrafast pathway analogous to the one previously found for the canonical (keto) form of cytosine+ . Dynamic electron correlation reduces the energy barrier in the keto form substantially (by ∼1 eV) but it is nevertheless still present. We additionally compute the UV/Vis absorption signals of the structures encountered along these decay channels to provide spectroscopic fingerprints to assist future experiments in monitoring these intricate photo-processes.
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Affiliation(s)
- Javier Segarra‐Martí
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, 82 Wood LaneLondonW12 0BZUK
- Present address: Instituto de Ciencia MolecularUniversitat de ValenciaP.O. Box 22085ES-46071ValenciaSpain
| | - Michael J. Bearpark
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, 82 Wood LaneLondonW12 0BZUK
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8
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Deprotonation Dynamics of Guanine Radical Cations †. Photochem Photobiol 2021; 98:523-531. [PMID: 34653259 DOI: 10.1111/php.13540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
This review is dedicated to guanine radical cations (G+ )· that are precursors to oxidatively generated damage to DNA. (G+ )· are unstable in neutral aqueous solution and tend to lose a proton. The deprotonation process has been studied by time-resolved absorption experiments in which (G+ )· radicals are produced either by an electron abstraction reaction, using an external oxidant, or by low-energy/low-intensity photoionization of DNA. Both the position of the released proton and the dynamics of the process depend on the secondary DNA structure. While deprotonation in duplex DNA leads to (G-H1)· radicals, in guanine quadruplexes the (G-H2)· analogs are observed. Deprotonation in monomeric guanosine proceeds with a time constant of ˜60 ns; in genomic DNA, it is completed within 2 µs; and in guanine quadruplexes, it spans from at least 30 ns to over 50 µs. Such a deprotonation dynamics in four-stranded structures, extended over more than three decades of times, is correlated with the anisotropic structure of DNA and the mobility of its hydration shell. In this case, commonly used second-order reaction models are inappropriate for its description.
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Affiliation(s)
| | - Akos Banyasz
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France.,Univ Lyon, ENS de Lyon, CNRS, UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, Lyon, F-69342, France
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France
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9
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Balanikas E, Martinez-Fernandez L, Improta R, Podbevšek P, Baldacchino G, Markovitsi D. The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization. J Phys Chem Lett 2021; 12:8309-8313. [PMID: 34428044 DOI: 10.1021/acs.jpclett.1c01846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Guanine quadruplexes are four-stranded DNA/RNA structures composed of a guanine core (vertically stacked guanine tetrads) and peripheral groups (dangling ends and/or loops). Such a dual structural arrangement of the nucleobases favors their photoionization at energies significantly lower than the guanine ionization potential. This effect is important with respect to the oxidative DNA damage and for applications in the field of optoelectronics. Photoionization quantum yields, determined at 266 nm by nanosecond transient absorption spectroscopy, strongly depend on both the type and position of the peripheral nucleobases. The highest value (1.5 × 10-2) is found for the tetramolecular structure (AG4A)4 in which adenines are intermittently stacked on the adjacent guanine tetrads, as determined by nuclear magnetic resonance spectroscopy. Quantum chemistry calculations show that peripheral nucleobases interfere in a key step preceding electron ejection: charge separation, initiated by the population of charge transfer states during the relaxation of electronic excited states.
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Affiliation(s)
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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10
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The Two Faces of the Guanyl Radical: Molecular Context and Behavior. Molecules 2021; 26:molecules26123511. [PMID: 34207639 PMCID: PMC8227002 DOI: 10.3390/molecules26123511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.
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11
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Milovanović B, Stanković IM, Petković M, Etinski M. Modulating Excited Charge-Transfer States of G-Quartet Self-Assemblies by Earth Alkaline Cations and Hydration. J Phys Chem A 2020; 124:8101-8111. [DOI: 10.1021/acs.jpca.0c05022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11000, Serbia
| | - Ivana M. Stanković
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade 11000, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11000, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11000, Serbia
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12
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Balanikas E, Banyasz A, Douki T, Baldacchino G, Markovitsi D. Guanine Radicals Induced in DNA by Low-Energy Photoionization. Acc Chem Res 2020; 53:1511-1519. [PMID: 32786340 DOI: 10.1021/acs.accounts.0c00245] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Guanine (G) radicals are precursors to DNA oxidative damage, correlated with carcinogenesis and aging. During the past few years, we demonstrated clearly an intriguing effect: G radicals can be generated upon direct absorption of UV radiation with energy significantly lower than the G ionization potential. Using nanosecond transient absorption spectroscopy, we studied the primary species, ejected electrons and guanine radicals, which result from photoionization of various DNA systems in aqueous solution.The DNA propensity to undergo electron detachment at low photon energies greatly depends on its secondary structure. Undetected for monomers or unstacked oligomers, this propensity may be 1 order of magnitude higher for G-quadruplexes than for duplexes. The experimental results suggest nonvertical processes, associated with the relaxation of electronic excited states. Theoretical studies are required to validate the mechanism and determine the factors that come into play. Such a mechanism, which may be operative over a broad excitation wavelength range, explains the occurrence of oxidative damage observed upon UVB and UVA irradiation.Quantification of G radical populations and their time evolution questions some widespread views. It appears that G radicals may be generated with the same probability as pyrimidine dimers, which are considered to be the major lesions induced upon absorption of low-energy UV radiation by DNA. As most radical cations undergo deprotonation, the vast majority of the final reaction products is expected to stem from long-lived deprotonated radicals. Consequently, when G radical cations are involved, the widely used oxidation marker 8-oxodG is not representative of the oxidative damage.Beyond the biological consequences, photogeneration of electron holes in G-quadruplexes may inspire applications in nanoelectronics; although four-stranded structures are currently studied as molecular wires, their behavior as photoconductors has not been explored so far.In the present Account, after highlighting some key experimental issues, we first describe the photoionization process, and then, we focus on radicals. We use as show-cases new results obtained for genomic DNA and Oxytricha G-quadruplexes. Generation and reaction dynamics of G radicals in these systems provide a representative picture of the phenomena reported previously for duplexes and G-quadruplexes, respectively.
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Affiliation(s)
| | - Akos Banyasz
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble France
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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13
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Semmeq A, Badawi M, Hasnaoui A, Ouaskit S, Monari A. DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets. Chemistry 2020; 26:11340-11344. [PMID: 32511805 DOI: 10.1002/chem.202002025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/04/2020] [Indexed: 11/07/2022]
Abstract
The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.
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Affiliation(s)
- Abderrahmane Semmeq
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France.,Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Michael Badawi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Abdellatif Hasnaoui
- LS3M, Faculté Polydisicplinaire-Khouribga, University Sultan Moulay Slimane of Beni Mellal, B.P 145, 25000, Khouribga, Morocco
| | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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14
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions. Molecules 2020; 25:molecules25092094. [PMID: 32365780 PMCID: PMC7248781 DOI: 10.3390/molecules25092094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
The study deals with the primary species, ejected electrons, and guanine radicals, leading to oxidative damage, that is generated in four-stranded DNA structures (guanine quadruplexes) following photo-ionization by low-energy UV radiation. Performed by nanosecond transient absorption spectroscopy with 266 nm excitation, it focusses on quadruplexes formed by folding of GGG(TTAGGG)3 single strands in the presence of K+ ions, TEL21/K+. The quantum yield for one-photon ionization (9.4 × 10-3) was found to be twice as high as that reported previously for TEL21/Na+. The overall population of guanine radicals decayed faster, their half times being, respectively, 1.4 and 6.7 ms. Deprotonation of radical cations extended over four orders of magnitude of time; the faster step, concerning 40% of their population, was completed within 500 ns. A reaction intermediate, issued from radicals, whose absorption spectrum peaked around 390 nm, was detected.
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Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
| | - Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
- Correspondence: ; Tel.: +33-169084644
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15
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Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
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