Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase

Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.     

Chemical bonding in phosphane and amine complexes of main group elements and transition metals

The geometries and bond dissociation energies of the main group complexes X3B-NX3, X3B-PX3, X3Al-NX3, and X3Al-PX3 (X = H, Me, Cl) and the transition metal complexes (CO)5M-NX3 and (CO)5M-PX3 (M = Cr, Mo, W) have been calculated using gradient-corrected density functional theory at the BP86/TZ2P level. The nature of the donor-acceptor bonds was investigated with an energy decomposition analysis. It is found that the bond dissociation energy is not a good measure for the intrinsic strength of Lewis acidity and basicity because the preparation energies of the fragments may significantly change the trend of the bond strength. The interaction energies between the frozen fragments of the borane complexes are in most cases larger than the interaction energies of the alane complexes. The bond dissociation energy of the alane complexes is sometimes higher than that of the borane analogues because the energy for distorting the planar equilibrium geometry of BX3 to the pyramidal from in the complexes is higher than for AlX3. Inspection of the three energy terms, DeltaE(Pauli), DeltaE(orb), and DeltaE(elstat), shows that all three of them must be considered to understand the trends of the Lewis acid and base strength. The orbital term of the donor-acceptor bonds with the Lewis bases NCl3 and PCl3 have a higher pi character than the bonds of EH3 and EMe3, but NCl3 and PCl3 are weaker Lewis bases because the lone-pair orbital at the donor atoms N and P has a high percent s character. The calculated DeltaE(int) values suggest that the trends of the intrinsic Lewis bases' strengths in the main-group complexes with BX3 and AlX3 are NMe3 > NH3 > NCl3 and PMe3 > PH3 > PCl3. The transition metal complexes exhibit a somewhat different order with NH3 > NMe3 > NCl3 and PMe3 > PH3 > PCl3. The slightly weaker bonding of NMe3 than that of NH3 comes from stronger Pauli repulsion. The bond length does not always correlate with the bond dissociation energy, nor does it always correlate with the intrinsic interaction energy.     

New three-step domino reaction, "thiophilic addition-beta-elimination of fluoride-[3,3] sigmatropic rearrangement": Synthesis of alpha-allylic and alpha,alpha-bis(allylic) alpha-trifluoromethyl dithioesters

The three-step domino reaction, "thiophilic addition of an organomagnesium reagent onto dithioester-beta-elimination of fluoride-[3,3] sigmatropic rearrangement", provides the product of formal regiospecific substitution of a fluorine atom by an allyl group. This mild and versatile methodology was applied to the synthesis of various alpha-allylic and alpha,alpha-bis(allylic) alpha-trifluoromethyl dithioesters.     

In situ characterisation of a microorganism surface by Raman microspectroscopy: the shell of Ascaris eggs

Intestinal nematodes are very common human parasites and a single species, Ascaris lumbricoïdes, is estimated to infect a quarter of the world’s population. A sticky external layer covers their eggs. This work shows that Raman vibrational confocal spectroscopy is able to give information on the biochemical composition of the shell of Ascaris eggs. The biochemical localised characterisation of Ascaris eggs was performed directly on the eggs in their aqueous environment. The studied parasites came from two origins: dissections of adult females and extractions from biosolid sludges. The presence of mucopolysaccharides, proteins and chitin in the shell was demonstrated. The presence of ascaroside compounds was shown particularly via the narrow and intense bands from the organised long CH₂ chains. To the best of our knowledge, this is the first time that the latter have been observed in Raman vibrational spectra of microorganisms. Hydration of the shell was different depending on the intensity of the colour of the sludge eggs. Knowledge of the biochemical structural properties of egg surfaces would be useful to understand the egg adhesion phenomena on vegetables contaminated by reused wastewater.     

An algorithmic construction of group automorphisms and the quantum Yang-Baxter equation

The structure group G of a non-degenerate symmetric set (X,S) is a Bieberbach and a Garside group. We describe a combinatorial method to compute explicitly a group of automorphisms of G and show this group admits a subgroup that preserves the Garside structure. In some special cases, we could also prove the group of automorphisms found is an outer automorphism group.     

Large deviations for Brownian motion in a random scenery

We prove large deviations principles in large time, for the Brownian occupation time in random scenery . The random field is constant on the elements of a partition of ^d into unit cubes. These random constants, say consist of i.i.d. bounded variables, independent of the Brownian motion {B_s,s0}. This model is a time-continuous version of Kesten and Spitzer's random walk in random scenery. We prove large deviations principles in ``quenched' and ``annealed' settings.Mathematics Subject Classification (2000):60F10, 60J55, 60K37     

Synthesis of amphiphilic phenylazophenyl glycosides and a study of their liquid crystal properties

Several 4-(4'-N,N-didodecylaminophenylazo)phenyl 1,2-trans glycosides 5a-e with various carbohydrate heads (beta-D-gluco, beta-D-galacto, beta-lacto, beta-D-xylo, and alpha-D-manno) have been synthesized. The key step was the formation of phenyldiazonium tetrafluoroborates 2a-e from the per-O-acetylated 4-aminophenyl glycosides 1a-e. These salts were condensed with N,N-didodecylaniline under phase transfer conditions and the per-O-acetylated 4-(4'-N,N-didodecylaminophenylazo)phenyl 1,2-trans glycosides 4a-e were fully de-O-acetylated by the Zemplén method. The self-organizing liquid crystal properties of the compounds were investigated by a variety of techniques, including polarized light microscopy, differential scanning calorimetry, and X-ray diffraction. All but one of the materials exhibited smectic A, lamellar phases. Remarkably, the glucose derivative exhibited a rectangular disordered columnar phase. This result has implications with respect to the induced curvature created by the recognition processes of the glucose headgroup relative to the other sugar moieties and to the prevalence of various glycolipids in cell membranes     

Multi-step reactions of N-monosubstituted (polyfluoroalkane)thioamides with alkyllithium reagents

Reactions of N-alkyl- or N-aryl(perfluoroalkyl)thiocarboxamides with alkyl lithium reagents are described. Trifluorothioacetamides are converted into the corresponding lithium salts. Compounds bearing a long polyfluorinated chain terminated by a CHF₂ group and compounds containing an N-alkyl substituent with a proton adjacent to nitrogen react further via a multi-step reaction sequence involving HF elimination and then vinylic fluorine substitution and/or S_N′ type fluorine substitution. These transformations led to unsaturated N-monosubstituted polyfluorinated thioamides.     

Efficient mutation detection in MEN1 gene using a combination of single-strand conformation polymorphism (MDGA) and heteroduplex analysis

For facilitated genotypic analysis of multiple endocrine neoplasia type 1 (MEN1), a familial syndrome associated with tumors of the parathyroid and neuroendocrine tissues, we developed two screening methods, heteroduplex mutation assay (HMA) and mutation detection gel analysis (MDGA), both based on electrophoretic discrimination of polymerase chain reaction (PCR) products, to detect the mutations. Forty-three genomic DNA samples were used for the evaluation of these techniques. The whole coding region of MEN1 was PCR-amplified with fluorescent primers and then denatured/renatured before electrophoresis on an automated sequencer. 100% of the mutations were detected, subsequently confirmed and identified by sequencing. "Negative" samples were used to evaluate the specificity and reproducibility of the two techniques. The combination of the two methods allows high throughput cost-effective mutation screening which is less laborious than systematic sequencing of the whole coding region of MEN1. Together, these methods provide an efficient screen for MEN1 mutations.     

Monitoring protein interactions in the living cell through the fluorescence decays of the cyan fluorescent protein.

Using fluorescence lifetime microspectroscopy and imaging techniques, we have studied the fluorescence of cyan fluorescent protein (CFP) transiently expressed in HEK-293 cells, in the presence or absence of its fluorescence resonance energy transfer (FRET) partner, yellow fluorescent protein (YFP). When the two proteins are attached through a 27-amino-acid linker, a 33 % average efficiency of intramolecular energy transfer is accurately determined inside the cell. Additionally, we observe a systematic quenching of the CFP fluorescence with increasing levels of protein expression. This quenching cannot be accounted for by formation of the previously described dimer of GFP-related proteins, since its magnitude is unchanged when the fluorescent proteins carry the mutation A206K shown to dissociate this dimer in vitro. Even when the intracellular protein concentration largely exceeds the in vitro dissociation constant of the dimer, self-association remains undetectable, either between free proteins or intramolecularly within the CFP-YFP construct. Instead, the detailed concentration effects are satisfactorily accounted for by a model of intermolecular, concentration-dependent energy transfer, arising from molecular proximity and crowding. In the case of CFP alone, we suggest that self-quenching could result from a pseudo-homo FRET mechanism between different, spectrally shifted emissive forms of the protein. These phenomena require careful consideration in intracellular FRET studies.