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Flaviviruses are enveloped viruses causing high public concerns. Their maturation spans several cellular compartments having different pH. Thus, complex control mechanisms are in place to avoid premature maturation. Here we report the dynamical behavior at neutral and acidic pH of the precursor of the membrane fusion protein E of tick-borne encephalitis, showing the different stabilization of the E dimer and the role played by the small fusion-assisting protomer (pr). The comprehension, at atomic resolution, of the fine regulation of viral maturation will be fundamental to the development of efficient strategies against emerging viral threats.

The diastereoselective assembly of achiral constituents through a single spontaneous process into complex covalent architectures bearing multiple stereogenic elements still remains a challenge for synthetic chemists. Here, we show that such an extreme level of control can be achieved by implementing stereo-electronic information on synthetic organic building blocks and templates and that non-directional interactions (i.e., electrostatic and steric interactions) can transfer this information to deliver, after self-assembly, high-molecular weight macrocyclic species carrying up to 16 stereogenic elements. Beyond the field of supramolecular chemistry, this proof of concept should stimulate the on-demand production of highly structured polyfunctional architectures.

Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.

Calixarenes are hallmark molecules in supramolecular chemistry as guest cages for small ligands. They have also conversely proved their interest as auxiliary ligands toward assisted co-crystallization of proteins. These functionalized macromolecular cages target positively-charges residues, and notably surface-exposed lysines, with a site-selectivity finely characterized experimentally, but that remains to be assessed. Relying on a tailored molecular dynamics simulations protocol, we explore the association of para-sulfonato-calix[4]arenes with an antifungal protein, as a small yet most competitive system with 13 surface-exposed lysines. Our computational approach probe "de novo" the electrostatically-driven interaction, ruled out by a competition with salt bridges, not only corroborating the main binding site probed by X-ray, but also characterizing a second binding site that can act as a transient hub spot. The attach-pull-release (APR) method provides a very good assessment of the overall binding free energy measured experimentally (-6.42+-0.5 vs -5.45 kcal.mol-1 by isothermal titration calorimetry). This work also probes dynamical allosteric modifications upon ligand binding, and our computational protocol could be generalized to situate the supramolecular forces ruling out the calixarene-assisted co-crystallization of proteins.

Non-structural accessory proteins in viruses play a key role in hijacking the basic cellular mechanisms, which is essential to promote the virus survival and evasion of the immune system. The immonuglobulin-like open reading frame 8 (ORF8) protein expressed by SARS-CoV-2 accumulates in the nucleus and may influence the regulation of the gene expression in infected cells. In this contribution, by using micro-second time-scale all-atom molecular dynamics simulations, we unravel the structural bases behind the epigenetic action of ORF8. In particular, we highlight how the protein is able to form stable aggregates with DNA through a histone tail-like motif, and how this interaction is influenced by post-translational modifications, such as acetylation and methylation, which are known epigenetic markers in histones. Our work not only clarifies the molecular mechanisms behind the perturbation of the epigenetic regulation caused by the viral infection, but also offers an unusual perspective which may foster the development of original antivirals.

The STimulator of INterferon Genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP upon the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines which are crucial for protecting cells from infections. STING signaling pathway can also influence both tumor-suppressive and tumor-promoting mechanisms, rendering it an appealing target for drug design. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the differential molecular mechanisms exhibited by these variants is of utmost importance notably towards personalized medicine treatments against diseases such as viral infections (COVID-19, Dengue…), cancers, or auto-inflammatory diseases. Owing to micro-seconds scale molecular modeling simulations and post-processing by contacts analysis and Machine Learning techniques, we reveal the dynamical behavior of four STING variants (wild type, G230A, R293Q, and G230A-R293Q) and we rationalize the variability of efficiency observed experimentally. Our results show that the decrease of STING activity is linked to a stiffening of key-structural features of the binding cavity, together with changes of the interaction patterns within the protein.

International audience; Polyazanes (that is, higher nuclearity homologues of hydrazines) with increasing numbers of bound nitrogen atoms (from 3 to 5) were prepared via additions of lower order polyazanes to diazo reagents, including the first pentazane ever described. A structure was obtained. It was shown that the polynitrogen chains adopt a helical conformation. DFT modeling shows that the arrangement subsists in solution. While the polyazanes are all reducing agents, they become less so with the increasing number of nitrogens.

International audience

International audience; We take advantage of the near-resonant enhancement of the third-order nonlinear response to engineer a two-photon polymerization photoinitiator with optimized efficiency in regard with literature benchmarks. We study in detail its linear and resonant third-order nonlinear optical properties, with a particular focus on photoinduced radical generation. Careful choice of peripheral substituents enable its direct solubilization into a mixture of commercial multifunctional acrylic monomers, resulting in homogeneous photoresist with good optical transparency upon simple mixing. When submitted to sub-nanosecond pulsed laser irradiation at 532 nm, the resulting photoresist displays a polymerization threshold up to eight times lower than that obtained with classically used two-photon initiators, giving rise to sub-100 nm linewidth at 250 nm interline separation, and resulting in highly defined threedimensional (3D) structures.

Correction for ‘Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures’ by Marco Deiana et al., Nanoscale, 2021, 13, 13795–13808, https://doi.org/10.1039/D1NR02855C.

International audience; Lanthanide complexes are now widely used as powerful auxiliaries for protein crystallisation to improve the crucial nucleation and phasing steps. We systematically analysed the influence of the commercial crystallisation kit composition on the efficiency of two lanthanide additives [Na]$_3$[Eu(DPA)$_3$] and Tb-Xo4, we developed. This study revealed that our initial the trisdipicolinate complex presents a lower chemical stability and a strong tendency to self-crystallisation detrimental for its use in highthroughput robotised crystallisation platform. In particular, we reported herein the crystal structures of (Mg(H$_2$O)$_6$)$_3$ [Eu(DPA)$_3$]$_2$•7H$_2$O (1),{(Ca(H$_2$O)$_4$)$_3$[Eu(DPA)$_3$]$_2$}$_n$•11nH$_2$O (2) and {Cu(DPA)(H$_2$O)$_2$}$_n$ (3) resulting from spontaneous crystallisation in the presence of divalent alkaline earth cation or transmetallation. On the other hand, the Tb-Xo4 is perfectly soluble in the crystallisation media, stable in the presence of alkaline-earth dications and slowly decomposed (within days) by trans-metalation with transition metals. The original structure of [Tb$_4$L$_4$(H$_2$O)$_4$]Cl$_4$•15H$_2$O (4) is also described. In this article, we also discussed the potential beneficial interactions between the crystallisation mixture components and Tb-Xo4 leading to the formation of more complex adducts observed in the case of the AdKA protein crystallisation, like {AdkA/Tb-Xo4/Mg$^{2+}$ /glycerol} in the protein binding sites. The observation of such multi-components adducts illustrates the complexity and the versatility of the supramolecular chemistry occurring at the surface of proteins.

Singlet-triplet interconversions (intersystem crossing, ISC) in organic molecules are at the basis of many important processes in cutting-edge photonic applications (organic light-emitting devices, photodynamic therapy, etc.). Selection rules for these transitions are mainly governed by the spin-orbit coupling (SOC) phenomenon. Although the SOC relies on complex relativistic phenomena, theoreticians have, with time, developed increasingly sophisticated and efficient approaches to gain access to a satisfactory evaluation of its magnitude. However, recent works have highlighted the remarkable and somehow unexpected efficiency of dimers of small conjugated molecules in terms of ISC quantum yields, whose origin has not been completely investigated. In this work, we bring a coupled experimental and theoretical analysis of the origin of the unusually large ISC efficiency on a series of such dimers that differ by their nature (covalent or supramolecular). We show that considering the dynamical nature of the SOC, and especially its dependence on angular orientations between the dimer subunits sometimes overlooked in the literature, it is necessary to rationalize some counterintuitive experimental observations. This combined experimental and theoretical work paves the way for new molecular engineering rules for SOC control.

Several urea-inserted organo-polyoxometalates (POMs) derived from polyoxotungstovanadate [P2 V3 W15 O61 ]9- were prepared. The insertion of the carbonyl into the polyoxometallic framework activates the urea toward Hydrogen-bond catalysis. This was shown on the Friedel-Crafts arylation of trans-β-nitrostyrene. Modelling shows that the most stable form of the organo-POMs features a cis-trans arrangement of the two N-H bonds, but that the likely catalytically active trans-trans form is accessible at room temperature. Finally, it is possible that the oxo substituents next to the vanadium atoms may help the approach of the nucleophile via H-bonding.

Stimuli-responsive self-assembled molecular materials are currently subject to intense research activity. This growing interest stems largely from the myriad of exciting applications envisioned for dynamic supramolecular assemblies, also known as dynamers, in materials science, sensing, catalysis and electronics. Enormous technologic interests are for instance at stake in being able to devise molecular objects that could respond to external stimuli by changes in structure and function. These particular properties can lead to applications in various domains as (i) in molecular electronics, (ii) in analytic science, with switchable hosts allowing the controlled binding/release of pollutants or drugs, (iii) in materials science with the development of adaptive supramolecular polymers. Our group has been focusing over the past few years on the development of tailor-made redox-controllable molecular and supramolecular systems involving electrogenerated pi-radicals as key responsive and/or assembling elements [1, 2]. In this lecture, we will focus on the physico-chemical properties of a series of porphyrin-based molecular tectons whose self-assembly can be controlled with optical or electrical stimulus. The dynamic properties of these stimuli-responsive molecular architectures and molecular materials will mainly be discussed on the basis of electrochemical, spectroelectrochemical and ESR experiments supported by quantum chemical calculations [3-6]. References : [1] C. Kahlfuss, E. Saint-Aman, C. Bucher (2016). Redox-controlled intramolecular motions triggered by π-dimerization and πmerization processes In T. Nishinaga (Ed.), Organic Redox Systems: Synthesis, Properties, and Applications (pp. 39). New-York: John Wiley and sons. [2] H. D. Correia, S. Chowdhury, A. P. Ramos, L. Guy, G. J.-F. Demets, C. Bucher, Polymer International 68, 572 (2019). [3] S. Chowdhury, Y. Nassar, L. Guy, D. Frath, F. Chevallier, E. Dumont, A. P. Ramos, G. J.-F. Demets, C. Bucher, Electrochimica Acta 316, 79 (2019). [4] C. Kahlfuss, S. Denis-Quanquin, N. Calin, E. Dumont, M. Garavelli, G. Royal, S. Cobo, E. Saint-Aman, C. Bucher, Journal of the American Chemical Society 138, 15234−15242 (2016). [5] C. Kahlfuss, T. Gibaud, S. Denis-Quanquin, S. Chowdhury, G. Royal, F. Chevallier, E. Saint-Aman, C. Bucher, Chemistry - A European Journal 24, 13009 (2018). [6] C. Kahlfuss, R. Gruber, E. Dumont, G. Royal, F. Chevallier, E. Saint-Aman, C. Bucher, Chemistry - A European Journal 25, 1573 (2019). Figure 1

Phosphate recognition in water is a hot topic due to their importance in biology and environment. The design and conception of water-soluble receptors that are efficient and selective is a difficult task because of the water medium, which provides highly competitive electrostatic interactions. A possible strategy relies on multipoint recognition with a polycationic site for electrostatic interaction with the phosphate moiety and a hydrophobic cavity for the organic one. Following this strategy, a detailed study of the hosting properties of a water-soluble resorcinarene-based metallo-cavitand, WRim4Zn, with various organophosphates is presented. The ZnII receptor showed good affinity and selectivity for n-alkyl phosphates (CnP) having from 2 to 6 carbons, in 100% water at physiological pH. The strongest association was obtained with C6P [K′pD7.4 = 3.6 × 104 M−1] whereas C7P binds 100 times less strongly. This very sharp selectivity pattern stands in strong contrast with carboxylate guests for which the optimum size corresponds to acetate. The different selectivity pattern stems from a switch in the coordination mode of ZnII upon phosphate binding, inducing the decoordination of two out of the four imidazole arms grafted on the resorcinarene macrocycle. Hence, the efficiency of WRim4Zn for alkyl phosphate recognition and unusual selectivity relative to the organic moiety of the phosphate analytes is ascribed to the synergistic action of a metal binding site for the phosphate head (the ZnII receptor is 100 times more efficient than the cavity ligand WRim4 itself), a hydrophobic cavity for alkyl embedment, protonated arms leading to further electrostatic stabilization, spacers between the recognition points (ZnII, imidazoliums, resorcinarene bowl cavity) allowing directional and spatial control of guest binding. Another key point is the water-solubility of the hydrophobic core insured by the pyridinium feet positioned away from the receptacle, which avoids the destructuring of the receptor metallo-site. Phosphodiesters, which are singly charged and congested, are not recognized. Hence, the good affinity displayed for C6P makes WRim4Zn one of the best cavity-based receptor for organophosphates described to date. These results open new routes for sensing biologically and environmentally important organic anions, considering the tunability of the functionalization pattern of the resorcinarene core.

DNA-protein cross-links constitute bulky DNA lesions that interfere with the cellular machinery. Amongst these stable covalently tethered adducts, the efficient nucleophilic addition of the free amino group of lysines onto the guanine radical cation has been evidenced. In vitro addition of a trilysine peptide onto a guanine radical cation generated in a TGT oligonucleotide is so efficient that competitive addition of a water molecule, giving rise to 8-oxo-7,8-dihydroguanine, is not observed. This suggests a spatial proximity between guanine and lysine for the stabilization of the prereactive complex. We report all-atom microsecond scale molecular dynamics simulations that probe the structure and interactions of the trilysine peptide (KKK) with two oligonucleotides. Our simulations reveal a strong, electrostatically driven yet dynamic interaction, spanning several association modes. Furthermore, the presence of neighbouring cytosines has been identified as a factor favoring KKK binding. Relying on ab initio molecular dynamics on a model system constituted of guanine and methylammonium, we also corroborate a mechanistic pathway involving fast deprotonation of the guanine radical cation followed by hydrogen transfer from ammonium leaving as a result a nitrogen reactive species that can subsequently cross-link with guanine. Our study sheds new light on a ubiquitous mechanism for DNA-protein cross-links also stressing out possible sequence dependences.

Sequence dependence of the (6–4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.

International audience; A metal-induced self-assembly strategy is used to promote the π-dimerization of viologen-based radicals at room temperature and in standard concentration ranges. Discrete box-shaped 2:2 (M:L) macrocycles or coordination polymers are formed in solution by self-assembly of a viologen-based ditopic ligand with cis-[Pd(en)(NO3)2], trans-[Pd(CH3CN)2(Cl)2], or [Pd(CH3CN)4(BF4)2]. Changing the redox state of the bipyridium units involved in the tectons, from their dicationic state to their radical cation state, results in a reversible “inflation/deflation” of the discrete 2:2 (M:L) macrocyclic assemblies associated to a large modification in the size of their inner cavity. Viologen-centered electron transfer is also used to trigger a dissociation of the coordination polymers formed with tetrakis(acetonitrile)Pd(II), the driving force of the disassembling process being the formation of discrete box-shaped 2:2 (M:L) assemblies stabilized by π-dimerization of both viologen cation radicals.

Apurinic/apyrimidinic sites are the most common DNA damage under physiological conditions. Yet, their structural and dynamical behavior within nucleosome core particles has just begun to be investigated, and show dramatic differences with the one of abasic sites in B-DNA. Clusters of two or more abasic sites are repaired even less efficiently and hence constitute hotspots of high mutagenicity notably due to enhanced double-strand breaks formation. Based on a X-ray structure of a 146-bp DNA wrapped onto a histone core, we investigate the structural behavior of two bistranded abasic sites positioned at mutational hotspots along microsecond-range molecular dynamics simulations. Our simulations allow us to probe histone tails interactions at clustered abasic sites locations, with a definitive assignment of the key residues in-volved in the NCP-catalyzed formation of DNA–protein cross-linking in line with recent experimental findings, and pave the way towards a systematic assessment of histone tails response to DNA lesions.

International audience; Highlights• We calculated radical production around gold/water nanoparticle (GNP/WNP) in water.• Calculations were performed for single keV photon absorption.• In the micrometer range, radicals are overproduced by GNP compared to WNP.• In the nanometer range, radicals are overproduced by small GNP compared to WNP due to Auger electrons.• In the nanometer range, radical production is comparable for large NP.

The combination of several closely spaced DNA lesions, which can be induced by a single radical hit, constitutes a hallmark in the DNA damage landscape and radiation chemistry. The occurrence of such tandem base lesions give rise to a strong coupling with the double helix degrees of freedom and induce important structural deformations, in contrast to DNA strands containing a single oxidized nucleobase. Although such complex lesions are known to be refractory to repair by DNA glycosylases, there is still a lack of structural evidence to rationalize these phenomena. In this contribution, we explore, by numerical modeling and molecular simulations, the behavior of the bacterial glycosylase responsible for base excision repair (MutM), specialized in excising oxidatively-damaged defects such as 7,8-dihydro-8-oxoguanine (8-oxoG). The difference in lesion recognition between a simple damage and a tandem lesions featuring an additional abasic site is assessed at atomistic resolution owing to microsecond molecular dynamics simulation and machine learning postprocessing, allowing to extensively pinpoint crucial differences in the interaction patterns of the damaged bases. This work advocates for the use of such high throughput numerical simulations for exploring the complex combinatorial chemistry of tandem DNA lesions repair and more generally multiple damaged sites of the utmost significance in radiation chemistry.

International audience; In a previous work, we extended and benchmarked the MDM Monte Carlo code with available data for gold metallic media irradiated by electron beams. In this paper, we worked with the aim of improving the cross sections on which our Monte Carlo simulation is based, and which are essential for an accurate description of the transport of electrons in gold. The mesoscopic potential of solid gold has been predicted, and its sensitivity toward electron emission has been evaluated. This potential was derived from the calculation of the electrostatic and atomistic potential by density functional theory and used to calculate inelastic inverse mean free path for electron transport. After integrating these results into our Monte Carlo code, we evaluated the impact of these new cross sections on yields of electron emission from solid gold irradiated by monoenergetic electron beams. We obtained a mesoscopic potential value of − 12.77 eV for our model of bulk metal gold, 27% lower than the one commonly estimated from the Fermi energy. This result impacted on the inverse mean free path for plasmon excitations with a 10% decrease for electrons in the range of 6–30 eV. Regarding electron emission yields, there was no impact of the new mesoscopic potential on the primary electron yields, but for secondary electrons, the emission yields were increased by a factor of up to two depending on the primary beam energy and thickness of the gold foil.

International audience; Light-activated functional materials capable of remote control over duplex and G-quadruplex (G4) nucleic acids formation at the cellular level are still very rare. Herein, we report on the photoinduced macrocyclisation of a helicenoid quinoline derivative of binaphthol that selectively provides easy access to an unprecedented class of extended heteroaromatic structures with remarkable photophysical and DNA/RNA binding properties. Thus, while the native bisquinoline precursor shows no DNA binding activity, the new in situ photochemically generated probe features high association constants to DNA and RNA G4s. The latter inhibits DNA synthesis by selectively stabilizing G4 structures associated with oncogenic promoters and telomere repeat units. Finally, the light sensitive compound is capable of in cellulo photoconversion, localizes primarily in the G4-rich sites of cancer cells, competes with a well-known G4 binder and shows a clear nuclear co-localization with the quadruplex specific antibody BG4. This work provides a benchmark for the future design and development of a brand-new generation of light-activated target-selective G4binders. † Electronic supplementary information (ESI) available: Synthesis, NMR spectra, HPLC, theoretical studies, spectra associated with the study of the photochemical reactions, G4 binding studies, cell imaging and quantification. See

Sequence dependence of the (6-4)photoproduct dynamics when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing a different upstream and downstream flexibilities. Moreover, REST2 simulations allow to probe structures possibly important for damaged DNA recognition.

In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex–protein interaction or self-assembly processes.

DNA is constantly exposed to external and metabolic stress agents, including the solar radiation and in particular the UV portion of the electromagnetic spectrum. Such source of stress can induce photochemical modification of the structure of DNA and of its basic components, i.e. the nucleobases. DNA lesions may ultimately lead to genomic instability, mutations, and even to carcinogenesis. Hence, cells dispose of complex biochemical repair pathways in charge of remove the DNA lesions and avoid their accumulation. In this Chapter, we present the complexity of the DNA lesion chemical and structural space, also complicated by the intricate coupling with the biological relevant signaling pathways. Through some relevant examples, we will show how proper multiscale simulation protocols can provide a unified picture of the complex phenomena and hence answer biological relevant questions, paving the way to a veritable computational photobiology approach.

Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links leading to strand breaks, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the frequency of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. Such an in silico mapping of DNA-protein cross-links gives important insights for further experimental studies involving mutagenesis and truncation of histone tails to unravel mechanisms of DPCs formation.

The pyrimidine-pyrimidone (6-4) photoproduct (64-PP) is an important photoinduced DNA lesion, which constitutes a mutational signature for melanoma. The structural impact of 64-PP on DNA complexed with compaction proteins, and notably histones, affects the mechanism of its mutagenicity and repair but remains poorly understood. Here we investigate the conformational dynamics of DNA containing 64-PP lesions within the nucleosome core particle by atomic-resolution molecular dynamics simulations at the multi-microsecond time scale. We demonstrate that the histone core exerts important mechanical restraints that largely decrease global DNA structural fluctuations. However, we also show that local DNA flexibility at the damaged site is enhanced, due to imperfect structural adaptation to restraints imposed by the histone core. In particular, if 64-PP faces the histone core and is therefore not directly accessible by the repair protein, the complementary strand facing the solvent exhibits higher flexibility than the corresponding strand in a naked, undamaged DNA. This may serve as an initial recognition signal for repair. Our simulations also pinpoint the structural role of proximal residues from the truncated histone tails.

Synthesis of novel photoinitiators, spectroscopic (UV vis, fluorescence, steady state and time resolved), electrochemical and EPR studies of their photoinduced radical generation mechanisms, Z-scan measurements of their two-photon absorption cross section, two-photon polymerization at 532 nm, with a pulsed ns laser, material evaluation by scanning electron microscopy

International audience; The use of gold nanoparticles to enhance radiation therapy efficiency has been thoroughly investigated over the past two decades. While theoretical studies have mostly focused on physical mechanisms and dose enhancement, studies of free radical production are scarce. In this work, we investigated the primary yield of free radicals ( and ) induced by 20–90 keV monoenergetic photons, for small GNPs concentrations. Our study is based on a Monte Carlo approach which enables electron transport down to low energy, both in water and in gold. We obtained, for a gold concentration of 1 , an average chemical enhancement varying from 6 to 14%, depending mostly on the photon energy and, to a lesser extent, on the chemical species and size of the GNP. This enhancement is strongly correlated to the dose deposition enhancement, although not strictly proportional. While supporting the hypothesis that therapeutic efficiency of GNPs may not simply be explained by an overproduction of free radicals in the early stage, our simulation provides inputs for further macroscopic simulations, including cumulative track effects and potentially GNP chemical reactivity.

Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge residue between the two main anchoring sites. In addition,the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of theprotein.

International audience; Functionalized gold nanoparticles are investigated by density functional theory calculations in the context of cancer radiotherapy. Several typical experimental shapes, including nanostars, nanospheres, and nanorods, are modeled by optimizing Au clusters covered by organic monolayers composed of hydrated short-chain polyethylene glycol (PEG) ligands. The PEGylation stabilizes significantly the stellation of decahedral Au54 by deforming significantly its geometry at the spikes. The higher stability of the PEG molecules adsorbed on this stellated nanocluster with respect to the more spherical icosahedral Au55 and Au79 leads to a larger energy cost to desorb them and thus a weaker propensity for the starred nanoparticle to exchange ligands with the cell membrane, in agreement with experiments. These results open interesting possibilities for advancing our understanding of the cellular uptake of gold nanoparticles.

Protein crystals with their precise, periodic array of functional building blocks have potential applications in biomaterials, sensing, and catalysis. This paper describes how a highly porous crystalline framework of a cationic redox protein and an anionic macrocycle can be modulated by a small cationic effector. Ternary composites of protein (∼13 kDa), calix[8]arene (∼1.5 kDa), and effector (∼0.2 kDa) formed distinct crystalline architectures, dependent on the effector concentration and the crystallization technique. A combination of X-ray crystallography and density functional theory (DFT) calculations was used to decipher the framework variations, which appear to be dependent on a calixarene conformation change mediated by the effector. This “switch” calixarene was observed in three states, each of which is associated with a different interaction network. Two structures obtained by co-crystallization with the effector contained an additional protein “pillar”, resulting in framework duplication and decreased porosity. These results suggest how protein assembly can be engineered by supramolecular host–guest interactions. This research was supported by NUI Galway, the SYSPROD project (AXELERA Pôle de Compétitivité) and Science Foundation Ireland (Grant No. 13/CDA/2168 to PBC). We thank SOLEIL synchrotron (Paris) for beam time allocation, and the staff at beamline PROXIMA-2A for their assistance with data collection. peer-reviewed 2020-09-06

International audience; The present poster reports on the formation and on the electrochemical/spectroscopic characterization of inclusion complexes formed in aqueous media between cucurbit[7 or 8]urils cavitands (CB[7], CB[8]) and a rigid four-pointed star-shaped viologen-appended porphyrin tecton. The formation of discrete 4:1 pseudo-rotaxane-like caviplexes, involving threading of CB[n] rings on the rigid viologen-based star’s branches has been demonstrated by nuclear magnetic resonance and mass spectrometry measurements. Then, the photo- and redox-triggered formation of 2D supramolecular assemblies involving CB[8]s and the four electron reduced tectons as key building elements, has been established on the ground of in-depth electrochemical and spectroscopic analyses supported by quantum calculations. The CB[8]-promoted intermolecular p-dimerization of the viologen cation radicals introduced at the meso positions of the porphyrin plateform has been brought to light through the diagnostic signatures of the 1:2 host-guest ternary caviplexes formed between viologen and CB[8] and by spectroscopic data collected after electrochemical, chemical or photochemical reduction of the viologen-based tectons. The CB[8] hosts not only proved useful to promote the redox-triggered formation of supramolecular assemblies, it was also found to prevent the chemical reduction of the porphyrin ring in aqueous media and its subsequent conversion into phlorin products.

International audience; Solvated gold nanoparticles have been modeled in the fluxional regime by density functional theory including dispersion forces for an extensive set of conventional morphologies. The study of isolated adsorption of one water molecule shows that the most stable adsorption forms are similar (corners and edges) regardless of the nanoparticle shape and size, although the adsorption strength differs significantly (0.15 eV). When a complete and explicit water solvation shell interacts with gold nanoclusters, metastable in vacuum and presenting a predominance of (100) square facets (ino-decahedra Au55 and Au147), these nanoparticles are found unstable and transform into the closest morphologies exhibiting mainly (111) triangular facets and symmetries. The corresponding adsorption strength per water molecule becomes independent of shape and size and is enhanced by the formation of two hydrogen bonds on average. For applications in radiotherapy, this study suggests that the shapes of small gold nanoparticles should be homogenized by interacting with the biological environment.

International audience; A halogen-bond templated 11 macrocyclization in solution is reported. Tetra(iodoperfluorophenyl) ethers were used as halogen-bonded exotemplates in a substoichiometric amount (5 mol %). Pyridine-containing macrocyclic architectures were formed by ruthenium-catalyzed tandem metathesis/transfer hydrogenation sequence using sodium borohydride and methanol as non-dihydrogen hydrogen source. The halogen-bonded stabilization energies were analyzed relying on density functional theory.

The Dawson tungstovanadate [P2 W15 V3 O62 ](9-) can be grafted to secondary diolamides. The electron-withdrawing character of the polyanion increases the acidity of the amide proton, leading to an organo-polyoxometalate, which can be used as a Bronsted organocatalyst. High-field NMR and DFT modeling indicate that the amide proton stays on the nitrogen and that the exalted acidity derives from the interaction between the organic and inorganic parts of the organo-polyoxometalate. The amide-inserted vanadotungstates thus form a new family of (hybrid) heteropolyacids, offering new perspectives for the application of POM-based catalysis in organic synthesis.

International audience; DNA photosensitization is one of the physical processes behind photodynamic therapy techniques, i.e. the combined use of photoactive drugs and visible radiation for therapeutical purposes. In this contribution we report the analysis of the photophysical properties of a two-photon absorption dye together with its interaction with DNA. The linear and non-linear optical properties are modeled taking into account the complex environment including dynamic and vibrational effects. It is also clearly demonstrated that the excited state manifold may evolve toward spontaneous photoionization with the production of a solvated electron. In turn both the radical cation and the solvated electron may react with the DNA backbone to produce a strand break; hence we have characterized a phototherapeutic dye that absorbs in the infrared region and is able to work under hypoxidic conditions, i.e. a prodrug of great interest for the potential treatment of solid tumors.

We report the investigation of the thermochemical properties of benzophenone interacting with B-DNA studied by all-atom molecular dynamic simulations. In particular, we determine the binding free energy for two competitive binding modes, minor groove binding and double insertion. Our results allow us to quantitatively resolve for the first time the mode of binding of this paradigmatic photosensitizer, indicating a marked preference for minor groove binding. Furthermore, we have settled a protocol allowing for the determination of binding energies in the case of non-covalent interaction with DNA, in particular, tackling the non-trivial problem of the strong reorganization of the DNA imposing extended statistical sampling. Our contribution paves the way to the systematic determination of the thermochemical properties of drugs or pollutants interacting with DNA.