Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation

A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.     

Synthesis,Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications

There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures.     

Stereocontrolled access to isoprostanes via a bicyclo[3.3.0]octene framework

We report a simple and highly stereocontrolled strategy toward the total synthesis of isoprostanes based on a bicyclic alpha,beta-epoxy ketone intermediate 6. Bicyclo[3.3.0]octene scaffold permitted stereodirection of reagents allowing stereoselective epoxidation, diastereoselective ketone reduction, and regioselective epoxide opening otherwise not accessible with a simple cyclopentene framework.     

Isotope effects in liquid water by infrared spectroscopy. II. Factor analysis of the temperature effect on H2O and D2O

Some 500 infrared (IR) spectra of light and heavy waters were obtained between 29 and 93 degrees C in order to identify the species present in liquid water. Factor analysis of these gives two species for each type of water with their IR spectra and abundance curves. Using an orthogonalization procedure, we obtained the temperature factor limits of -22 and +118 degrees C (+/-5 degrees C) that we coined cold and hot factors, respectively. Within experimental error, these limits are the same for light and heavy waters. The spectra of the orthogonalized factors presented show a decrease of the OH (OD) stretch band integrated intensities of almost 36% from the cold to the hot factors. No "free" OH (OD) group is present or formed in the temperature ramp. This indicates that all water molecules in the bulk are made of an oxygen atom surrounded with four hydrogen atoms, two covalently bonded, and two hydrogen bonded. This is consistent with the previous study of mixtures of H(2)O and D(2)O [part I: J.-J. Max and C. Chapados, J. Chem. Phys. 116, 4626 (2002)]. To maintain the ordinary liquid within the limits of 0 and 100 degrees C at atmospheric pressure, a fraction of the cold and hot factors are necessary. With the spectra of the cold and hot factors and the abundance curves, one can generate the spectrum at any temperature between -22 and +118 degrees C of light and heavy liquid waters.     

Theoretical and experimental studies of enflurane. Infrared spectra in solution, in low-temperature argon matrix and blue shifts resulting from dimerization

Theoretical studies are performed on enflurane (CHFCl-CF(2)-O-CHF(2)) to investigate the conformational properties and vibrational spectra. Calculations are carried out at the B3LYP/6-31G(d) level along with a natural bond orbital (NBO) analysis. Experimental infrared spectra are investigated in carbon tetrachloride solution at room temperature and in argon matrix at 12 K. In agreement with previously reported data (Pfeiffer, A.; Mack, H.-G.; Oberhammer, H. J. Am. Chem. Soc. 1998, 120, 6384), it is shown that the four most stable conformers possess a trans configuration of the C-C-O-C skeleton and a gauche orientation of the CHF(2) group (with respect to the central C-O bond). These conformations are favored by electrostatic interaction between the H atom of the CHF(2) group and the F atoms of the central CF(2) group. Hyperconjugation effects from the O lone pairs to the antibonding orbitals of the neighboring C-H and C-F bonds also contribute to the stability of the four conformers. The vibrational frequencies, infrared intensities, and potential energy distributions are calculated at the same level of theory for the most stable conformers. On the basis of the theoretical results, these conformers are identified in an argon matrix. The influence of the concentration on the nu(CH) vibrations suggests the formations of higher aggregates in solution. Theoretical calculations are carried out on the enflurane dimer. The results show that the dimer is formed between two enflurane conformers having the largest stability. The dimer has an asymmetric cyclic structure, the two enflurane molecules being held together by two nonequivalent C-H...F hydrogen bonds, the C-H bond of the CHFCl group acting as a proton donor, and one of the F atoms of the CHF(2) groups acting as a proton acceptor. The theory predicts a contraction of 0.0014-0.0025 A of the two CH bonds involved in the interaction along with a blue shift of 30-38 cm(-1) of the corresponding nu(C-H) bands, in good agreement with the blue shifts of 35-39 cm(-1) observed in an argon matrix.     

One-Pot Regioselective γ-Trifluoromethylthiolation and γ-Methylthiolation of Enals

We describe herein the direct electrophilic γ-trifluoromethylthiolation and γ-methylthiolation of enals, via the in situ formation of the corresponding silyl dienol ether. This one-pot process is carried out under simple and mild reaction conditions and is compatible with a variety of functional groups.     

Diastereocontrolled addition of organometallic reagents to S-chiral N-(tert-butanesulfinyl)-α-fluoroenimines

Grignard and organolithium reagents efficiently react with (S)-N-(tert-butanesulfinyl)-α-fluoroenimines to provide chiral allylamines in excellent yields and with diastereomeric ratios of up to 96:4. Acidic removal of the sulfinyl group and simple functional group transformations allow to get enantiopure fluoroolefin dipeptide mimics.     

Oxidation kinetics of methylhydrazine in a strictly single-phase medium studied in reconstituted air

The oxidation of methylhydrazine (monomethylhydrazine MMH) is studied in a strictly single-phase gaseous medium, in a reconstituted surrounding atmosphere. In order to work under such conditions, a specific apparatus was assembled to monitor the evolution of the reactants through time. The reaction kinetics was studied at 50°C to avoid condensation of the water formed and for O₂/MMH mole ratios between 1 and 4. Under these conditions, the partial pressures of O₂ were between 0.05 and 0.18 bar (4% MMH per volume). The main reaction products were monitored through time and identified by gas chromatography coupled with mass spectrometry (GC/MS). The products were: N₂, CH₄, CH₃-NH-N=CH₂ (formaldehyde monomethylhydrazone), NH₃, H₂O, CH₃OH, and CH₂=N-N=N-CH₃ (2,3,4-triazapenta-1,3-diene). The formation of nitrosamines was not observed under these experimental conditions. The rate laws related to the disappearance of the reagents were clearly established and can be described by 2 consecutive parallel reactions of order 2 whose rate constants are: k ₁ = 7.57 × 10⁻² bar⁻¹ min⁻¹ and k ₂ = 0.5 bar⁻¹ min⁻¹. Analysis of the products permitted establishing an approximated balance of the global reaction.