Publications by authors named "Akos Banyasz"

35 Publications

Deprotonation Dynamics of Guanine Radical Cations.

Photochem Photobiol 2021 Oct 15. Epub 2021 Oct 15.

Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France.

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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http://dx.doi.org/10.1111/php.13540DOI Listing
October 2021

3D Printing and Pyrolysis of Optical ZrO Nanostructures by Two-Photon Lithography: Reduced Shrinkage and Crystallization Mediated by Nanoparticles Seeds.

Small 2021 10 14;17(42):e2102486. Epub 2021 Sep 14.

Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université de Lyon 1, 46 allée d'Italie, Lyon, 69364, France.

Two-photon lithography is a potential route to produce high-resolution 3D ceramics. However, the large shrinkage due to the elimination of an important organic counterpart of the printed material during debinding/sintering remains a lock to further development of this technology. To limit this phenomenon, an original approach based on a composite resin incorporating 45 wt% ultrasmall (5 nm) zirconia stabilized nanoparticles into the zirconium acrylate precursor is proposed to process 3D zirconia microlattices and nanostructured optical surfaces. Interestingly, the nanoparticles are used both as seeds allowing control of the crystallographic phase formed during the calcination process and as structural stabilizing agent preventing important shrinkage of the printed ceramic. After 3D photolithography and pyrolysis, the weight and volume loss of the microstructures are drastically reduced as compared to similar systems processed with the reference resin without nanoparticles, and stable 3D microstructures of cubic zirconia are obtained with high spatial resolution. In the case of a patterned surface, the refractive index of 2.1 leads to a diffraction efficiency large enough to obtain microfocusing with linewidths of 0.1 µm, and the demonstration of a microlens array with a period as small as 0.8 µm.
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http://dx.doi.org/10.1002/smll.202102486DOI Listing
October 2021

Hybrid multimodal contrast agent for multiscale investigation of neuroinflammation.

Nanoscale 2021 Feb;13(6):3767-3781

Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Université Lyon 1, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France.

Neuroinflammation is a process common to several brain pathologies. Despites its medical relevance, it still remains poorly understood; there is therefore a need to develop new in vivo preclinical imaging strategies to monitor inflammatory processes longitudinally. We here present the development of a hybrid imaging nanoprobe named NP3, that was specifically designed to get internalized by phagocytic cells and imaged in vivo with MRI and bi-photon microscopy. NP3 is composed of a 16 nm core of gadolinium fluoride (GdF3), coated with bisphosphonate polyethylene glycol (PEG) and functionalized with a Lemke-type fluorophore. It has a hydrodynamic diameter of 28 ± 8 nm and a zeta potential of -42 ± 6 mV. The MR relaxivity ratio at 7 T is r1/r2 = 20; therefore, NP3 is well suited as a T2/T2* contrast agent. In vitro cytotoxicity assessments performed on four human cell lines revealed no toxic effects of NP3. In addition, NP3 is internalized by macrophages in vitro without inducing inflammation or cytotoxicity. In vivo, uptake of NP3 has been observed in the spleen and the liver. NP3 has a prolonged vascular remanence, which is an advantage for macrophage uptake in vivo. The proof-of-concept that NP3 may be used as a contrast agent targeting phagocytic cells is provided in an animal model of ischemic stroke in transgenic CX3CR1-GFP/+ mice using three complementary imaging modalities: MRI, intravital two-photon microscopy and phase contrast imaging with synchrotron X-rays. In summary, NP3 is a promising preclinical tool for the multiscale and multimodal investigation of neuroinflammation.
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http://dx.doi.org/10.1039/d0nr07026bDOI Listing
February 2021

Two-Photon Absorbing AIEgens: Influence of Stereoconfiguration on Their Crystallinity and Spectroscopic Properties and Applications in Bioimaging.

ACS Appl Mater Interfaces 2020 Dec 20;12(49):55157-55168. Epub 2020 Nov 20.

Univ. Lyon, ENS Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie, UMR 5182, 46 Allée d'Italie, 69364 Lyon, France.

This paper aims at designing chromophores with efficient aggregation-induced emission (AIE) properties for two-photon fluorescence microscopy (2PFM), which is one of the best-suited types of microscopy for the imaging of living organisms or thick biological tissues. Tetraphenylethylene (TPE) derivatives are common building blocks in the design of chromophores with efficient AIE properties. Therefore, in this study, extended TPE AIEgens specifically optimized for two-photon absorption (2PA) are synthesized and the resulting (/) isomers are separated using chromatography on chiral supports. Comparative characterization of the AIE properties is performed on the pure () and () isomers and the mixture, allowing us, in combination with powder X-ray diffraction and solid-state NMR, to document a profound impact of crystallinity on solid-state fluorescence properties. In particular, we show that stereopure AIEgens form aggregates of superior crystallinity, which in turn exhibit a higher fluorescence quantum yield compared to diastereoisomers mixtures. Preparation of stereopure organic nanoparticles affords very bright fluorescent contrast agents, which are then used for cellular and intravital two-photon microscopy on human breast cancer cells and on zebrafish embryos.
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http://dx.doi.org/10.1021/acsami.0c15810DOI Listing
December 2020

Guanine Radicals Induced in DNA by Low-Energy Photoionization.

Acc Chem Res 2020 08 27;53(8):1511-1519. Epub 2020 Jul 27.

Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France.

Guanine () radicals are precursors to DNA oxidative damage, correlated with carcinogenesis and aging. During the past few years, we demonstrated clearly an intriguing effect: radicals can be generated upon direct absorption of UV radiation with energy significantly lower than the 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 -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 radical populations and their time evolution questions some widespread views. It appears that 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 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 -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 -quadruplexes. Generation and reaction dynamics of radicals in these systems provide a representative picture of the phenomena reported previously for duplexes and -quadruplexes, respectively.
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http://dx.doi.org/10.1021/acs.accounts.0c00245DOI Listing
August 2020

Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions.

Molecules 2020 Apr 30;25(9). Epub 2020 Apr 30.

LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.

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) single strands in the presence of K ions, . The quantum yield for one-photon ionization (9.4 × 10) was found to be twice as high as that reported previously for . 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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http://dx.doi.org/10.3390/molecules25092094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248781PMC
April 2020

Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by G-Quadruplexes and Modify Their Reactivity.

J Phys Chem Lett 2020 Feb 4;11(4):1305-1309. Epub 2020 Feb 4.

Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France.

G-Quadruplexes are formed by guanine rich DNA/RNA sequences in the presence of metal ions, which occupy the central cavity of these four-stranded structures. We show that these metal ions have a significant effect on the photogeneration and the reactivity of guanine radicals. Transient absorption experiments on G-quadruplexes formed by association of four TGGGGT strands in the presence of K reveal that the quantum yield of one-photon ionization at 266 nm (8.1 × 10) is twice as high as that determined in the presence of Na. Replacement of Na with K also suppresses one reaction path involving deprotonated radicals, (G-H2) → (G-H1) tautomerization. Such behavior shows that the underlying mechanisms are governed by dynamical processes, controlled by the mobility of metal ions, which is higher for Na than for K. These findings may contribute to our understanding of the ultraviolet-induced DNA damage and optimize optoelectronic devices based on four-stranded structures, beyond DNA.
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http://dx.doi.org/10.1021/acs.jpclett.9b03667DOI Listing
February 2020

Comprehensive Study of Guanine Excited State Relaxation and Photoreactivity in G-quadruplexes.

J Phys Chem Lett 2019 Nov 24;10(21):6873-6877. Epub 2019 Oct 24.

LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.

G-quadruplexes () are four-stranded DNA/RNA structures playing a key role in many biological functions and promising for nanotechnology applications. Here, combining theoretical calculations and multiscale time-resolved fluorescence, we describe, for the first time, an ensemble of photoactivated processes involving the guanines of the core. We use as showcase the formed by the human telomeric sequence GGG(TTAGGG) in the presence of Na ions. According to quantum mechanical/molecular mechanics calculations, the hyperchromism at the red part of the absorption spectrum, typical of structures, arises mainly from the inner Na ions. Various relaxation pathways, leading to excited states localized on individual bases, neutral excimers, and excited charge transfer states between two guanines or a guanine and a thymine in the loop, are mapped. Their fingerprints are detected in the fluorescence anisotropies and the fluorescence decays, spanning five decades of time. Finally, a reaction funnel leading to guanine dimerization is identified.
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http://dx.doi.org/10.1021/acs.jpclett.9b02740DOI Listing
November 2019

Populations and Dynamics of Guanine Radicals in DNA strands-Direct versus Indirect Generation.

Molecules 2019 Jun 26;24(13). Epub 2019 Jun 26.

LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.

Guanine radicals, known to be involved in the damage of the genetic code and aging, are studied by nanosecond transient absorption spectroscopy. They are generated in single, double and four-stranded structures (-quadruplexes) by one and two-photon ionization at 266 nm, corresponding to a photon energy lower than the ionization potential of nucleobases. The quantum yield of the one-photon process determined for telomeric G-quadruplexes () is (5.2 ± 0.3) × 10, significantly higher than that found for duplexes containing in their structure GGG and GG sequences, (2.1 ± 0.4) × 10. The radical population is quantified in respect of the ejected electrons. Deprotonation of radical cations gives rise to (H1) and (-H2) radicals for duplexes and -quadruplexes, respectively. The lifetimes of deprotonated radicals determined for a given secondary structure strongly depend on the base sequence. The multiscale non-exponential dynamics of these radicals are discussed in terms of inhomogeneity of the reaction space and continuous conformational motions. The deviation from classical kinetic models developed for homogeneous reaction conditions could also be one reason for discrepancies between the results obtained by photoionization and indirect oxidation, involving a bi-molecular reaction between an oxidant and the nucleic acid.
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http://dx.doi.org/10.3390/molecules24132347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651618PMC
June 2019

Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features.

J Phys Chem B 2019 06 31;123(23):4950-4957. Epub 2019 May 31.

LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.

G-quadruplexes are four-stranded DNA structures playing a key role in many biological functions and are promising for applications in the field of nanoelectronics. Characterizing the generation and fate of radical cations (electron holes) within these systems is important in relation to the DNA oxidative damage and/or conductivity issues. This study focuses on guanine radicals in G-quadruplexes formed by association of four TGGGGT strands in the presence of Na cations, (TG4T)/Na. Using nanosecond transient spectroscopy with 266 nm excitation, we quantitatively characterize hydrated ejected electrons and three types of guanine radicals. We show that, at an energy lower by 2.7 eV than the guanine ionization potential, one-photon ionization occurs with quantum yield of (3.5 ± 0.5) × 10. Deprotonation of the radical cations is completed within 20 μs, leading to the formation of (G-H2) radicals, following a strongly nonexponential decay pattern. Within 10 ms, the latter undergoes tautomerization to deprotonated (G-H1) radicals. The dynamics of the various radicals determined for (TG4T)/Na, in connection to those reported previously for telomeric G-quadruplexes TEL21/Na, is correlated with energetic factors computed by quantum chemical methods. The faster deprotonation of radical cations in (TG4T)/Na compared to TEL21/Na explains that irradiation of the former does not generate 8-oxodGuo, which is readily detected by high-performance liquid chromatography/mass spectrometry in the case of TEL21/Na.
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http://dx.doi.org/10.1021/acs.jpcb.9b02637DOI Listing
June 2019

A "Multi-Heavy-Atom" Approach toward Biphotonic Photosensitizers with Improved Singlet-Oxygen Generation Properties.

Chemistry 2019 Jul 30;25(38):9026-9034. Epub 2019 May 30.

Laboratoire de Chimie de l'ENS de Lyon, Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, 69342, Lyon, France.

Two trispicolinate 1,4,7-triazacyclonane (TACN)-based ligands bearing three picolinate biphotonic antennae were synthetized and their Yb and Gd complexes isolated. One series differs from the other by the absence (L )/presence (L ) of bromine atoms on the antenna backbone, offering respectively improved optical and singlet-oxygen generation properties. Photophysical properties of the ligands, complexes and micellar Pluronic suspensions were investigated. Complexes exhibit high two-photon absorption cross-section combined either with NIR emission (Yb) or excellent O generation (Gd). The very large intersystem crossing efficiency induced by the combination of bromine atom and heavy rare-earth element was corroborated with theoretical calculations. The O generation properties of L Gd micellar suspension under two-photon activation leads to tumour cell death, suggesting the potential of such structures for theranostic applications.
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http://dx.doi.org/10.1002/chem.201901047DOI Listing
July 2019

Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation.

Phys Chem Chem Phys 2018 Aug;20(33):21381-21389

LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.

Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.
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http://dx.doi.org/10.1039/c8cp02588fDOI Listing
August 2018

Topology Controls the Electronic Absorption and Delocalization of Electron Holes in Guanine Quadruplexes.

Chemistry 2018 Oct 13;24(57):15185-15189. Epub 2018 Sep 13.

LIDYL, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France.

Guanine quadruplexes (G4) are four-stranded DNA structures involved in biological processes and are promising candidates for potential nanotechnological applications. This study examines how the G4 topology affects the electronic absorption and the delocalization of electron holes, which play a key role in charge transport and oxidative damage. Combining transient absorption spectroscopy with PCM/TD-DFT calculations both parallel (P) and antiparallel (A) G4 are investigated, which are formed, respectively, by association of four TGGGGT strands and folding of the human telomeric sequence GGG(TTAGGG) . The experimental absorption spectra obtained upon photo-ionization of A and P are different. This is explained by the different topology of the two G4, as well as by hole delocalization between two stacked guanines, possible only in P . The spectral signature of delocalized hole in guanine-rich regions is provided and the chemical physical effects which rule the hole delocalization are discussed.
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http://dx.doi.org/10.1002/chem.201803222DOI Listing
October 2018

Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation.

Faraday Discuss 2018 04;207(0):181-197

LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.

There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.
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http://dx.doi.org/10.1039/c7fd00179gDOI Listing
April 2018

UV-induced damage to DNA: effect of cytosine methylation on pyrimidine dimerization.

Signal Transduct Target Ther 2017;2:17021. Epub 2017 Jun 9.

Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy.

Methylation/demethylation of cytosine plays an important role in epigenetic signaling, the reversibility of epigenetic modifications offering important opportunities for targeted therapies. Actually, methylated sites have been correlated with mutational hotspots detected in skin cancers. The present brief review discusses the physicochemical parameters underlying the specific ultraviolet-induced reactivity of methylated cytosine. It focuses on dimerization reactions giving rise to cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone adducts. According to recent studies, four conformational and electronic factors that are affected by cytosine methylation may control these reactions: the red-shift of the absorption spectrum, the lengthening of the excited state lifetime, changes in the sugar puckering modifying the stacking between reactive pyrimidines and an increase in the rigidity of duplexes favoring excitation energy transfer toward methylated pyrimidines.
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http://dx.doi.org/10.1038/sigtrans.2017.21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661629PMC
February 2021

Absorption of Low-Energy UV Radiation by Human Telomere G-Quadruplexes Generates Long-Lived Guanine Radical Cations.

J Am Chem Soc 2017 08 24;139(30):10561-10568. Epub 2017 Jul 24.

LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France.

Telomeres, which are involved in cell division, carcinogenesis, and aging and constitute important therapeutic targets, are prone to oxidative damage. This propensity has been correlated with the presence of guanine-rich sequences, capable of forming four-stranded DNA structures (G-quadruplexes). Here, we present the first study on oxidative damage of human telomere G-quadruplexes without mediation of external molecules. Our investigation has been performed for G-quadruplexes formed by folding of GGG(TTAGGG) single strands in buffered solutions containing Na cations (TEL21/Na). Associating nanosecond time-resolved spectroscopy and quantum mechanical calculations (TD-DFT), it focuses on the primary species, ejected electrons and guanine radicals, generated upon absorption of UV radiation directly by TEL21/Na. We show that, at 266 nm, corresponding to an energy significantly lower than the guanine ionization potential, the one-photon ionization quantum yield is 4.5 × 10. This value is comparable to that of cyclobutane thymine dimers (the major UV-induced lesions) in genomic DNA; the quantum yield of these dimers in TEL21/Na is found to be (1.1 ± 0.1) × 10. The fate of guanine radicals, generated in equivalent concentration with that of ejected electrons, is followed over 5 orders of magnitude of time. Such a quantitative approach reveals that an important part of radical cation population survives up to a few milliseconds, whereas radical cations produced by chemical oxidants in various DNA systems are known to deprotonate, at most, within a few microseconds. Under the same experimental conditions, neither one-photon ionization nor long-lived radical cations are detected for the telomere repeat TTAGGG in single-stranded configuration, showing that secondary structure plays a key role in these processes. Finally, two types of deprotonated radicals are identified: on the one hand, (G-H) radicals, stable at early times, and on the other hand, (G-H) radicals, appearing within a few milliseconds and decaying with a time constant of ∼50 ms.
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http://dx.doi.org/10.1021/jacs.7b05931DOI Listing
August 2017

Direct Oxidative Damage of Naked DNA Generated upon Absorption of UV Radiation by Nucleobases.

J Phys Chem Lett 2016 Oct 22;7(19):3945-3948. Epub 2016 Sep 22.

Université Grenoble Alpes, INAC-SCIB , F-38000 Grenoble, France.

It has been shown that in addition to formation of pyrimidine dimers, UV irradiation of DNA in the absence of photosensitizer also induces formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine, but the mechanism of formation of that oxidized base has not been clearly established. In the present study, we provide an unambiguous demonstration that absorption of UVC and UVB radiation by the nucleobases induces DNA oxidation via a direct process (one-electron oxidation) and not singlet oxygen. Evidence arose from the fact that polyamine-guanine adducts that are specifically produced through the transient formation of guanine radical cation are generated following UV irradiation of DNA in the presence of a polyamine even in the absence of any photosensitizer.
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http://dx.doi.org/10.1021/acs.jpclett.6b01781DOI Listing
October 2016

UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization.

J Phys Chem Lett 2016 Oct 22;7(19):3949-3953. Epub 2016 Sep 22.

LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France.

Adenyl radicals generated in DNA single and double strands, (dA) and (dA)·(dT), by one- and two-photon ionization by 266 nm laser pulses decay at 600 nm with half-times of 1.0 ± 0.1 and 4 ± 1 ms, respectively. Though ionization initially forms the cation radical, the radicals detected for (dA) are quantitatively identified as N6-deprotonated adenyl radicals by their absorption spectrum, which is computed quantum mechanically employing TD-DFT. Theoretical calculations show that deprotonation of the cation radical induces only weak spectral changes, in line with the spectra of the adenyl radical cation and the deprotonated radical trapped in low temperature glasses.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053904PMC
http://dx.doi.org/10.1021/acs.jpclett.6b01831DOI Listing
October 2016

Excited State Pathways Leading to Formation of Adenine Dimers.

J Phys Chem Lett 2016 06 18;7(11):2020-3. Epub 2016 May 18.

Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy.

The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine).
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http://dx.doi.org/10.1021/acs.jpclett.6b00660DOI Listing
June 2016

Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors.

J Phys Chem B 2016 05 2;120(18):4232-42. Epub 2016 May 2.

LIDYL, CEA, CNRS, Université Paris Saclay, F-91191 Gif-sur-Yvette, France.

C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs.
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http://dx.doi.org/10.1021/acs.jpcb.6b03340DOI Listing
May 2016

Effect of C5-methylation of cytosine on the photoreactivity of DNA: a joint experimental and computational study of TCG trinucleotides.

J Am Chem Soc 2014 Aug 25;136(31):10838-41. Epub 2014 Jul 25.

Istituto di Biostrutture e Bioimmagini-CNR , Via Mezzocannone 16, I-80134 Napoli, Italy.

DNA methylation, occurring at the 5 position of cytosine, is a natural process associated with mutational hotspots in skin tumors. By combining experimental techniques (optical spectroscopy, HPLC coupled to mass spectrometry) with theoretical methods (molecular dynamics, DFT/TD-DFT calculations in solution), we study trinucleotides with key sequences (TCG/T5mCG) in the UV-induced DNA damage. We show how the extra methyl, affecting the conformational equilibria and, hence, the electronic excited states, increases the quantum yield for the formation of cyclobutane dimers while reducing that of (6-4) adducts.
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http://dx.doi.org/10.1021/ja5040478DOI Listing
August 2014

Multi-pathway excited state relaxation of adenine oligomers in aqueous solution: a joint theoretical and experimental study.

Chemistry 2013 Mar 18;19(11):3762-74. Epub 2013 Jan 18.

CNRS, IRAMIS, SPAM, Laboratoire Francis Perrin, URA 2453 CEA/Saclay, 91191 Gif-sur-Yvette, France.

The singlet excited states of adenine oligomers, model systems widely used for the understanding of the interaction of ultraviolet radiation with DNA, are investigated by fluorescence spectroscopy and time-dependent (TD) DFT calculations. Fluorescence decays, fluorescence anisotropy decays, and time-resolved fluorescence spectra are recorded from the femtosecond to the nanosecond timescales for single strand (dA)20 in aqueous solution. These experimental observations and, in particular, the comparison of the fluorescence behavior upon UVC and UVA excitation allow the identification of various types of electronic transitions with different energy and polarization. Calculations performed for up to five stacked 9-methyladenines, taking into account the solvent, show that different excited states are responsible for the absorption in the UVC and UVA spectral domains. Independently of the number of bases, bright excitons may evolve toward two types of excited dimers having π-π* or charge-transfer character, each one distinguished by its own geometry and spectroscopic signature. According to the picture arising from the joint experimental and theoretical investigation, UVC-induced fluorescence contains contribution from 1) exciton states with a different degree of localization, decaying within a few ps, 2) "neutral" excited dimers decaying on the sub-nanosecond timescale, being the dominant species, and 3) charge-transfer states decaying on the nanosecond timescale. The majority of the photons emitted upon UVA excitation are related to charge-transfer states.
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http://dx.doi.org/10.1002/chem.201202741DOI Listing
March 2013

Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study.

J Am Chem Soc 2012 Sep 31;134(36):14834-45. Epub 2012 Aug 31.

CNRS, IRAMIS, SPAM, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France.

The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (T<>Ts) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (T<>Ts) and (6-4) adducts via different electronic excited states. T<>Ts are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.
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http://dx.doi.org/10.1021/ja304069fDOI Listing
September 2012

Base pairing enhances fluorescence and favors cyclobutane dimer formation induced upon absorption of UVA radiation by DNA.

J Am Chem Soc 2011 Apr 18;133(14):5163-5. Epub 2011 Mar 18.

CNRS, IRAMIS, SPAM, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France.

The photochemical properties of the DNA duplex (dA)(20)·(dT)(20) are compared with those of the parent single strands. It is shown that base pairing increases the probability of absorbing UVA photons, probably due to the formation of charge-transfer states. UVA excitation induces fluorescence peaking at ∼420 nm and decaying on the nanosecond time scale. The fluorescence quantum yield, the fluorescence lifetime, and the quantum yield for cyclobutane dimer formation increase upon base pairing. Such behavior contrasts with that of the UVC-induced processes.
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http://dx.doi.org/10.1021/ja110879mDOI Listing
April 2011

The peculiar spectral properties of amino-substituted uracils: a combined theoretical and experimental study.

J Phys Chem B 2010 Oct;114(39):12708-19

Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette.

A detailed experimental and computational study of the absorption and fluorescence spectra of 5-aminouracil (5 AU) and 6-aminouracil (6 AU) in aqueous solution is reported. The lowest energy band of the steady-state absorption spectra of 5 AU is considerably red-shifted, noticeably less intense, and broader than its counterpart in uracil (U). On the contrary, the 6 AU lowest energy absorption peak is close in energy to that of U, but it is much narrower and the transition is much more intense. The emission properties of 5 AU, 6 AU, and U are also very different. Both amino-substituted compounds exhibit indeed a much larger Stokes shift as compared to U, and the emission band of 5 AU is much narrower than that of 6 AU. Those features are fully rationalized with the help of PCM/TD-PBE0 calculations in aqueous solution and MS-CASPT2/CASSCF calculations in the gas phase. A stable minimum on the potential energy surface of the lowest energy bright state is found for 5 AU, both in the gas phase and in aqueous solution. For 6 AU a barrierless path leads to the conical intersection with the ground electronic state, but a nonplanar plateau region is predicted in aqueous solution, which is responsible for the very large Stokes shift. Some general considerations on the excited-state dynamics of uracil derivatives are also reported.
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http://dx.doi.org/10.1021/jp105267qDOI Listing
October 2010

UVA-induced cyclobutane pyrimidine dimers in DNA: a direct photochemical mechanism?

Org Biomol Chem 2010 Apr 4;8(7):1706-11. Epub 2010 Feb 4.

DSM/INAC/SCIB UMR-E 3 CEA/UJF FRE CNRS 3200/Laboratoire Lésions des Acides Nucléiques, CEA-Grenoble, France.

The carcinogenic action of UVA radiation is commonly attributed to DNA oxidation mediated by endogenous photosensitisers. Yet, it was recently shown that cyclobutane pyrimidine dimers (CPD), well known for their involvement in UVB genotoxicity, are produced in larger yield than oxidative lesions in UVA-irradiated cells and skin. In the present work, we gathered mechanistic information on this photoreaction by comparing formation of all possible bipyrimidine photoproducts upon UVA irradiation of cells, purified genomic DNA and dA(20):dT(20) oligonucleotide duplex. We observed that the distribution of photoproducts, characterized by the sole formation of CPD and the absence of (6-4) photoproducts was similar in the three types of samples. The CPD involving two thymines represented 90% of the amount of photoproducts. Moreover, the yields of formation of the DNA lesions were similar in cells and isolated DNA. In addition, the effect of the wavelength of the incident photons was found to be the same in isolated DNA and cells. This set of data shows that UVA-induced cyclobutane pyrimidine dimers are formed via a direct photochemical mechanism, without mediation of a cellular photosensitiser. This is possible because the double-stranded structure increases the capacity of DNA bases to absorb UVA photons, as evidenced in the case of the oligomer dA(20):dT(20). These results emphasize the need to consider UVA in the carcinogenic effects of sunlight. An efficient photoprotection is needed that can only be complete by completely blocking incident photons, rather than by systemic approaches such as antioxidant supplementation.
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http://dx.doi.org/10.1039/b924712bDOI Listing
April 2010

Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy.

J Phys Chem A 2010 Mar;114(9):3256-63

Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA Saclay, F-91191 Gif-sur-Yvette, France.

The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.
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http://dx.doi.org/10.1021/jp909410bDOI Listing
March 2010

Absorption of UV radiation by DNA: spatial and temporal features.

Mutat Res 2010 Apr-Jun;704(1-3):21-8. Epub 2009 Nov 24.

Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA/Saclay, F-91191 Gif-sur-Yvette, France.

The present review focuses on studies carried out by our group on the interaction of UV radiation with DNA. In particular, we examine the way that the energy acquired by DNA helices following direct absorption of UVC radiation is extended spatially and how its effects evolve during the time. These effects depend on the base sequence and can be revealed by the study of model helices. The experimental results were obtained by optical spectroscopy, used in a refined way which allows detection of very weak absorbance changes (10(-3)) as well as of intrinsic emission from DNA components whose fluorescence quantum yields are as low as 10(-4). Measurements were performed both under continuous irradiation and using pulsed excitation which permitted us to follow early events, occurring from 10(-14) to 10(-1)s. The experiments were guided by theoretical calculations. The spatial features concern the extent of the excited states formed immediately upon UV absorption; these were shown to be delocalized over several bases under the effect of electronic coupling. Moreover, thanks to the spectral fingerprints governed by the electronic coupling; we probed local denaturation induced on a double helix following formation of cyclobutane dimers. Regarding the temporal features, three different topics are presented: (i) ultrafast excitation energy transfer occurring among the bases in less than 100 fs, (ii) electron ejection from DNA upon absorption of one photon at 266 nm and (iii) formation of (6-4) photo-adducts involving a reaction intermediate. The most important message emerging from these studies is that DNA bases may adopt a collective behaviour versus UV radiation. Furthermore, time-resolved studies unravel processes which are undetectable by investigations using continuous irradiation. All these pieces of information change our understanding of how DNA damage occurs upon absorption of UV radiation.
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http://dx.doi.org/10.1016/j.mrrev.2009.11.003DOI Listing
August 2010

Effect of amino substitution on the excited state dynamics of uracil.

Photochem Photobiol Sci 2008 Jul 16;7(7):765-8. Epub 2008 May 16.

Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, Gif-sur-Yvette, France.

The excited state deactivation of two amino-substituted uracils, 5-aminouracil (5AU) and 6-aminouracil (6AU) in aqueous solution was studied by femtosecond fluorescence upconversion. The fluorescence of 6AU decays as fast as that of uracil with a unique time constant of about 100 femtoseconds. The fluorescence of 5AU exhibits a more complex behavior, fundamentally different from what we found in any other uracils: the decays are globally slower (up to several picoseconds) and depend strongly on the wavelength. This difference is attributed to the particular character of the amino group, affecting the out-of-plane motion of the 5-substituent which has been shown to be crucial for the ultrafast internal conversion occurring in uracils. Our observations indicate instead the formation of a transient fluorescent state which in turn is deactivated by a different relaxation process specific to the amino group.
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http://dx.doi.org/10.1039/b800764kDOI Listing
July 2008
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