Benoît Y. Michel

Experimental investigation of an innovative thermochemical process operating with a hydrate salt and moist air for thermal storage of solar energy: Global performance

This paper investigates an innovative open thermochemical system dedicated to high density and long term (seasonal) storage purposes. It involves a hydrate/water reactive pair and operates with moist air. This work focuses on the design of and experimentation with a large scale prototype using SrBr2/H2O as a reactive pair (400kg of hydrated salt, 105kWh of storage capacity and a reactor energy density of 203kWh/m3). Promising conclusions have been obtained regarding the feasibility and performance of such a storage process. Hydration specific powers from 0.75 to 2W/kg have been reached for a bed salt energy density of 388kWh/m3. Moreover, two important parameters that control the storage system have been identified and investigated: the equilibrium drop and the mass flow rate of moist air. Both have a strong influence on the reaction kinetics and therefore on the reactor’s thermal power.

Rational Design of a Solvatochromic Fluorescent Uracil Analogue with a Dual‐Band Ratiometric Response Based on 3‐Hydroxychromone

Fluorescent nucleoside analogues with strong and informative responses to their local environment are in urgent need for DNA research. In this work, the design, synthesis and investigation of a new solvatochromic ratiometric fluorophore compiled from 3-hydroxychromones (3HCs) and uracil fragments are reported. 3HC dyes are a class of multi-parametric, environment-sensitive fluorophores providing a ratiometric response due to the presence of two well-resolved bands in their emission spectra. The synthesized conjugate demonstrates not only the preservation but also the improvement of these properties. The absorption and fluorescence spectra are shifted to longer wavelengths together with an increase of brightness. Moreover, the two fluorescence bands are better resolved and provide ratiometric responses across a broader range of solvent polarities. To understand the photophysical properties of this new fluorophore, a series of model compounds were synthesized and comparatively investigated. The obtained data indicate that uracil and 3HC fragments of this derivative are coupled into an electronic conjugated system, which on excitation attains strong charge-transfer character. The developed fluorophore is a prospective label for nucleic acids. Abstract in Ukrainian: .

Small molecules DNA methyltransferases inhibitors

Methylation catalyzed by the DNA methyltransferases affects the C5 position of cytosine residues in DNA. This physiological process is active from the embryo conception, throughout all its developmental steps, and also later for the maintenance of the adult organism. Excess methylated cytosine in tumor suppressor genes is a consistent hallmark of human cancers. However, DNA methylation variation is now acknowledged to significantly contribute to genetic and common diseases. DNA methyltransferases became attractive therapeutic targets as DNA demethylation, in vitro, brought cancer cell differentiation and apoptosis. Inhibitors are already in use, alone or in combination, to treat myeloid malignancies, while clinical assays are ongoing for other diseases. DNA methylation and histone modifications are intimately correlated with epigenetic heritable modifications of gene expression that are independent of changes in the genetic sequence. Common initiatives for epigenetic research have built public databases with useful resources. The recent discovery of 5-hydroxymethyl cytosine has added new questions and challenges for the epigenome community. We review here knowledge about DNA methylation to provide researchers with the information needed to make more active inhibitors for the benefit of patients. Because of space limitations, many important works cannot be cited. We refer the reader to reviews containing these references.

Rational Design of Push-Pull Fluorene Dyes: Synthesis and Structure-Photophysics Relationship.

Our work surveyed experimental and theoretical investigations to construct highly emissive D-π-A (D=donor, A=acceptor) fluorenes. The synthetic routes were optimised to be concise and gram-scalable. The molecular design was first rationalised by varying the electron-withdrawing group from an aldehyde, ketotriazole or succinyl to methylenemalonitrile or benzothiadiazole. The electron-donating group was next varied from aliphatic or aromatic amines to saturated cyclic amines ranging from aziridine to azepane. Spectroscopic studies correlated with TD-DFT calculations provided the optimised structures. The selected push-pull dyes exhibited visible absorptions, significant brightness, important solvatofluorochromism, mega-Stokes shifts (>250 nm) and dramatic shifts in emission to the near-infrared. The current library includes the comprehensive characterization of 16 prospective dyes for fluorescence applications. Among them, several fluorene derivatives bearing different conjugation anchors were tested for coupling and demonstrated to preserve the photophysical responses once further bound.

Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues

Ratiometric and environment-sensitive fluorescent dyes present attractive advantages for sensing interactions in DNA research. Here, we report the rational design, synthesis, and photophysical characterization of 2-thienyl-, 2-furyl- and 2-phenyl-3-hydroxychromones bonded to the C-5 position of deoxyuridine. Since these two-color nucleosides were designed for incorporation into ODNs, we also investigated the sensitivity of the ratiometric response to hydration by using acetonitrile/water mixtures and neat solvents. The synthesized 2-thienyl and 2-furyl conjugates were found to exhibit more red-shifted absorption (by 31–36 nm) and emission (by 77–81 nm of the N* band), two-fold increased molar absorption coefficients, and dramatically enhanced (by 3–4.5 times) fluorescence quantum yields. Demonstrating a manifold increase in brightness, they preserve the ability of exquisite ratiometric responses to solvent polarity and hydration. This makes the new fluorescent nucleoside analogues highly relevant for subsequent labeling of the major groove in nucleic acids and sensing their interactions.

Air-Stable Pd Catalytic Systems for Sequential One-Pot Synthesis of Challenging Unsymmetrical Aminoaromatics

The selective functionalization of dibromoaromatic scaffolds using air-stable palladium catalytic systems was carried out. This methodology involved rapid mono and diselective Buchwald-Hartwig aminations via microwave irradiation. The conditions were optimized to couple sequentially different moieties in one pot. Couplings with a wide scope of amines allowed accessing a new library of symmetrical and unsymmetrical derivatives (35 examples). Using this versatile method, a near-IR push-pull sensor was prepared installing the electron-donating and -withdrawing groups through a multicomponent reaction. These conditions revealed to be gram-scalable and adaptable to various groups; hence, promoting facile use in synthetic chemistry.

Dynamics of Methylated Cytosine Flipping by UHRF1

DNA methylation patterns, which are critical for gene expression, are replicated by DNA methyltransferase 1 (DNMT1) and ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) proteins. This replication is initiated by the recognition of hemimethylated CpG sites and further flipping of methylated cytosines (mC) by the Set and Ring Associated (SRA) domain of UHRF1. Although crystallography has shed light on the mechanism of mC flipping by SRA, tools are required to monitor in real time how SRA reads DNA and flips the modified nucleobase. To accomplish this aim, we have utilized two distinct fluorescent nucleobase surrogates, 2-thienyl-3-hydroxychromone nucleoside (3HCnt) and thienoguanosine (thG), incorporated at different positions into hemimethylated (HM) and nonmethylated (NM) DNA duplexes. Large fluorescence changes were associated with mC flipping in HM duplexes, showing the outstanding sensitivity of both nucleobase surrogates to the small structural changes accompanying base flipping. Importantly, the nucleobase surrogates marginally affected the structure of the duplex and its affinity for SRA at positions where they were responsive to base flipping, illustrating their promise as nonperturbing probes for monitoring such events. Stopped-flow studies using these two distinct tools revealed the fast kinetics of SRA binding and sliding to NM duplexes, consistent with its reader role. In contrast, the kinetics of mC flipping was found to be much slower in HM duplexes, substantially increasing the lifetime of CpG-bound UHRF1, and thus the probability of recruiting DNMT1 to faithfully duplicate the DNA methylation profile. The fluorescence-based approach using these two different fluorescent nucleoside surrogates advances the mechanistic understanding of the UHRF1/DNMT1 tandem and the development of assays for the identification of base flipping inhibitors.

Dual emissive analogue of deoxyuridine as a sensitive hydration-reporting probe for discriminating mismatched from matched DNA and DNA/DNA from DNA/RNA duplexes

Fluorescent nucleosides with high sensitivity to H-bonding are of great interest not only to investigate DNA hydration and DNA–protein interactions and dynamics, but also to develop screening assays. Here, we report on the incorporation of a dual emissive uridine analogue based on the 3-hydroxychromone scaffold (3HC) into DNA oligonucleotides of different sequences and the characterization of the spectroscopic properties of the labelled oligonucleotides in matched and mismatched duplexes and in duplexes of different forms. The probe exhibits two-colour emission and spectral λ-shift, which vary as a function of the local hydration of the 3HC. It provides the highest sensitivity together with calibration on the molecular level, which allows discriminating between matched and mismatched dsDNA, as well as between B- and A-forms of DNA/DNA and DNA/RNA duplexes. We suggest that the physical basis of such behavior is the change of hydration in the close proximity of the fluorescent base emitter which appears ideally suitable for such sensing.

Turn-on Fluorene Push–Pull Probes with High Brightness and Photostability for Visualizing Lipid Order in Biomembranes

The rational design of environmentally sensitive dyes with superior properties is critical for elucidating the fundamental biological processes and understanding the biophysical behavior of cell membranes. In this study, a novel group of fluorene-based push-pull probes was developed for imaging membrane lipids. The design of these fluorogenic conjugates is based on a propioloyl linker to preserve the required spectroscopic features of the core dye. This versatile linker allowed the introduction of a polar deoxyribosyl head, a lipophilic chain, and an amphiphilic/anchoring group to tune the cell membrane binding and internalization. It was found that the deoxyribosyl head favored cell internalization and staining of intracellular membranes, whereas an amphiphilic anchor group ensured specific plasma membrane staining. The optimized fluorene probes presented a set of improvements as compared to commonly used environmentally sensitive membrane probe Laurdan such as red-shifted absorption matching the 405 nm diode laser excitation, a blue-green emission range complementary to the red fluorescent proteins, enhanced brightness and photostability, as well as preserved sensitivity to lipid order, as shown in model membranes and living cells.

Structural and Dynamical Impact of a Universal Fluorescent Nucleoside Analogue Inserted Into a DNA Duplex

Recently, a 3-hydroxychromone based nucleoside 3HCnt has been developed as a highly environment-sensitive nucleoside surrogate to investigate protein-DNA interactions. When it is incorporated in DNA, the probe is up to 50-fold brighter than 2-aminopurine, the reference fluorescent nucleoside. Although the insertion of 3HCnt in DNA was previously shown to not alter the overall DNA structure, the possibility of the probe inducing local effects cannot be ruled out. Hence, a systematic structural and dynamic study is required to unveil the 3HCnts limitations and to properly interpret the data obtained with this universal probe. Here, we investigated by NMR a 12-mer duplex, in which a central adenine was replaced by 3HCnt. The chemical shifts variations and nOe contacts revealed that the 3HCnt is well inserted in the DNA double helix with extensive stacking interactions with the neighbor base pairs. These observations are in excellent agreement with the steady-state and time-resolved fluorescence properties indicating that the 3HCnt fluorophore is protected from the solvent and does not exhibit rotational motion. The 3HCnt insertion in DNA is accompanied by the extrusion of the opposite nucleobase from the double helix. Molecular dynamics simulations using NMR-restraints demonstrated that 3HCnt fluorophore exhibits only translational dynamics. Taken together, our data showed an excellent intercalation of 3HCnt in the DNA double helix, which is accompanied by localized perturbations. This confirms 3HCnt as a highly promising tool for nucleic acid labeling and sensing.