Quantitative and sensitive detection of rare mutations using droplet-based microfluidics

Somatic mutations within tumoral DNA can be used as highly specific biomarkers to distinguish cancer cells from their normal counterparts. These DNA biomarkers are potentially useful for the diagnosis, prognosis, treatment and follow-up of patients. In order to have the required sensitivity and specificity to detect rare tumoral DNA in stool, blood, lymph and other patient samples, a simple, sensitive and quantitative procedure to measure the ratio of mutant to wild-type genes is required. However, techniques such as dual probe TaqMan(?) assays and pyrosequencing, while quantitative, cannot detect less than ～1% mutant genes in a background of non-mutated DNA from normal cells. Here we describe a procedure allowing the highly sensitive detection of mutated DNA in a quantitative manner within complex mixtures of DNA. The method is based on using a droplet-based microfluidic system to perform digital PCR in millions of picolitre droplets. Genomic DNA (gDNA) is compartmentalized in droplets at a concentration of less than one genome equivalent per droplet together with two TaqMan(?) probes, one specific for the mutant and the other for the wild-type DNA, which generate green and red fluorescent signals, respectively. After thermocycling, the ratio of mutant to wild-type genes is determined by counting the ratio of green to red droplets. We demonstrate the accurate and sensitive quantification of mutated KRAS oncogene in gDNA. The technique enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines and the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of unmutated KRAS genes. The sensitivity is only limited by the number of droplets analyzed. Furthermore, by one-to-one fusion of drops containing gDNA with any one of seven different types of droplets, each containing a TaqMan(?) probe specific for a different KRAS mutation, or wild-type KRAS, and an optical code, it was possible to screen the six common mutations in KRAS codon 12 in parallel in a single experiment.     

Synthesis,Photophysical, and Two‐Photon Absorption Properties of Elongated Phosphane Oxide and Sulfide Derivatives

A series of rod‐shaped and related three‐branched push–pull derivatives containing phosphane oxide or phosphane sulfide (PO or PS)—as an electron‐withdrawing group conjugated to electron‐donating groups, such as amino or ether groups, with a conjugated rod consisting of arylene–vinylene or arylene–ethynylene building blocks—were prepared. These compounds were efficiently synthesized by a Grignard reaction followed by Sonogashira coupling. Their photophysical properties including absorption, emission, time‐resolved fluorescence, and two‐photon absorption (TPA) were investigated with special attention to structure–property relationships. These fluorophores show high fluorescence quantum yields and solvent‐dependent experiments reveal that efficient intramolecular charge transfer occurs upon excitation, thereby leading to highly polar excited states, the polarity of which can be significantly enhanced by playing on the end groups and conjugated linker. Rod‐shaped and related three‐branched systems show similar fluorescence properties in agreement with excitation localization on one of the push–pull branches. By using stronger electron donors or replacing the arylene–ethynylene linkers with an arylene–vinylene one induces significant redshifts of both the low‐energy one‐photon absorption and TPA bands. Interestingly, a major enhancement in TPA responses is observed, whereas OPA intensities are only weakly affected. Similarly, phosphane oxide derivatives show similar OPA responses than the corresponding sulfides but their TPA responses are significantly larger. Finally, the electronic coupling between dipolar branches promoted by common PO or PS acceptor moieties induces either slight enhancement of the TPA responses or broadening of the TPA band in the near infrared (NIR) region. Such behavior markedly contrasts with triphenylamine‐core‐mediated coupling, which gives evidence for the different types of interactions between branches.     

Preparation of amphiphilic sucrose carbamates by reaction with alkyl isocyanates in water-alcohol mixtures

The reactivity of sucrose with isocyanates in aqueous media has been studied. Mixtures of water and alcohols allow good conversion of the isocyanates to sucrose carbamates. The influence of the reaction parameters on the selectivity (degree of substitution and regioselectivity) was investigated in the case of long chain isocyanates, which have potential surfactant properties.     

Acetate- and thiol-capped monodisperse ruthenium nanoparticles: XPS, XAS, and HRTEM studies

Monodisperse ruthenium nanoparticles were prepared by reduction of RuCl3 in 1,2-propanediol. The mean particle size was controlled by appropriate choice of the reduction temperature and the acetate ion concentration. Colloidal solutions in toluene were obtained by coating the metal particles with dodecanethiol. High-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XANES and EXAFS for the Ru K-absorption edge) were performed on particles of two different diameters, 2 and 4 nm, and in different environments, polyol/acetate or thiol. For particles stored in polyol/acetate XPS studies revealed superficial oxidation limited to one monolayer and a surface coating containing mostly acetate ions. Analysis of the EXAFS spectra showed both oxygen and ruthenium atoms around the ruthenium atoms with a Ru-Ru coordination number N smaller than the bulk value, as expected for fine particles. In the case of 2 nm acetate-capped particles N is consistent with particles made up of a metallic core and an oxidized monolayer. For 2 nm thiol-coated particles, a Ru-S bond was evidenced by XPS and XAS. For the 4 nm particles XANES and XPS studies showed that most of the ruthenium atoms are in the zerovalent state. Nevertheless, in both cases, when capped with thiol, the Ru-Ru coordination number inferred from EXAFS is much smaller than for particles of the same size stored in polyol. This is attributed to a structural disorganization of the particles by thiol chemisorption. HRTEM studies confirm the marked dependence of the structural properties of the ruthenium particles on their chemical environment; they show the acetate-coated particles to be single crystals, whereas the thiol-coated particles appear to be polycrystalline.     

Reactivity of atomic cobalt with molecular oxygen: a combined IR matrix isolation and theoretical study of the formation and structure of CoO2

The reactivity of atomic cobalt toward molecular oxygen in rare gas matrices has been reinvestigated. Experiments confirm that Co atoms in their a(4)F ground state are inert toward O(2) in solid argon and neon but reactive in the b(4)F first excited state, in agreement with the previous gas-phase study of Honma and co-workers. The formation of CoO(2) starting from effusive beams of Co and O(2) has been followed by IR absorption spectroscopy, both in neon and argon matrices. Our observations show that only the dioxo form, OCoO, is stabilized in the matrix and that IR absorptions previously assigned to the peroxo and superoxo forms are due to other, larger species. The present data strongly support the linear geometry in rare gas matrices proposed by Weltner and co-workers. We report on measurements on all IR-active fundamental modes for (16)OCo(16)O, (18)OCo(18)O, and (16)OCo(18)O with additional combination transitions supplying anharmonicity correction. This allows for a 5.93 +/- 0.02 mdyne/A CoO harmonic bond force constant in solid neon. Using the empirical relationship previously optimized for the CoO diatomics, an approximate value for the CoO internuclear bond distance is proposed (1.615 +/- 0.01A). In light of recent theoretical studies predicting (2)A(1) or (6)A(1) electronic ground states, the geometry and electronic structure of the OCoO molecule has also been reconsidered. Calculations carried out at the CCSD(T)/6-311G(3df) level indicate a linear structure with an r(e) = 1.62 A bond distance, consistent with the experimental estimate. For later studies of larger systems, where CCSD(T) calculations become too time-consuming, an effective DFT-based method is proposed which reproduces the basic electronic and geometrical properties of cobalt dioxide. Quantitative results are compared to the experimental data and high-level results regarding bond length and frequencies. This DFT method is used to propose a reaction pathway.     

Modulation of hydrophobic effect by cosolutes

This work concerns a comparison of the hydration properties and self-association behavior in aqueous solution of three biologically relevant simple molecules: tert-butyl alcohol (TBA), trimethylamine-n-oxide (TMAO), and glycine betaine (GB). These molecules were used as a model to study hydrophobic behavior in water solutions. In particular, water perturbation induced by TBA, TMAO, and GB molecules was studied as a function of the solute molar fraction X(2) (0 < X(2) < 0.04) by Raman spectra of water in the fundamental OH-stretching region (3,800-2,800 cm(-1)). Furthermore, possible hydrophobic clustering of these molecules was investigated by studying the behavior of the alkyl CH stretching band in the 3,100-2,900 cm(-1) frequency region as a function of X(2). To establish the existence of a correlation between the effects of these three solutes on the micellization process and changes in the properties of the solvent, the behavior of the critical micelle concentration of sodium dodecyl sulfate was also investigated as a function of the added amount of TBA, TMAO, and GB. On the whole, these data show that there is no direct correlation between a solute's effect on the water structure and its effect on micelle or protein stability. Results indicate that, while TBA starts to self-aggregate at approximately X(2) = 0.025, both TMAO and GB do not exhibit any significant self-aggregation up to the highest concentration considered. In addition, nonadditive perturbations of the H-bonded networks of solvent water are observed in the case of TBA solutions, but are absent in both the TMAO and GB cases. The absence of these nonlinear effects in TMAO and GB water solutions allow for tracing the microscopical mechanism of the neutrality of these osmolytes toward hydrophobic effects. This confers the compatibility to these two osmolytes, which can be accumulated at high concentrations without interfering with biochemical processes in the cell.     

Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques

Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.     

Experimental/theoretical electrostatic properties of a styrylquinoline-type HIV-1 integrase inhibitor and its progenitors

We have established that polyhydroxylated styrylquinolines are potent inhibitors of HIV-1 integrase (IN). Among them, we have identified (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinolinecarboxylic acid (1) as a promising lead. Previous molecular dynamics simulations and docking procedures have shown that the inhibitory activity involves one or two metal cations (Mg2+), which are present in the vicinity of the active center of the enzyme. However, such methods are generally based on a force-field approach and still remain not as reliable as ab initio calculations with extended basis sets on the whole system. To go further in this area, the aim of the present study was to evaluate the predictive ability of the electron density and electrostatic properties in the structure-activity relationships of this class of HIV-1 antiviral drugs. The electron properties of the two chemical progenitors of 1 were derived from both high-resolution X-ray diffraction experiments and ab initio calculations. The twinning phenomenon and solvent disorder were observed during the crystal structure determination of 1. Molecule 1 exhibits a planar s-trans conformation, and a zwitterionic form in the crystalline state is obtained. This geometry was used for ab initio calculations, which were performed to characterize the electronic properties of 1. The electron densities, electrostatic potentials, and atomic charges of 1 and its progenitors are here compared and analyzed. The experimental and theoretical deformation density bond peaks are very comparable for the two progenitors. However, the experimental electrostatic potential is strongly affected by the crystal field and cannot straightforwardly be used as a predictive index. The weak difference in the theoretical electron densities between 1 and its progenitors reveals that each component of 1 conserves its intrinsic properties, an assumption reinforced by a 13C NMR study. This is also shown through an excellent correlation of the atomic charges for the common fragments. The electrostatic potential minima in zwitterionic and nonzwitterionic forms of 1 are discussed in relation with the localization of possible metal chelation sites.     

The Schrödinger Equation Type with a Nonelliptic Operator

We consider some linear Schrödinger equation with variable coefficients associated to a smooth symmetric metric g which can be degenerate, without sign and such that g has a submatrix of fixed rank v which is uniformly nondegenerate. In this general setting we prove Strichartz estimates with a loss of derivative on the solution. We also discuss the problem of the control of high frequencies. In particular, we prove that if the equation preserves the H ^s norm for all s ≥ 0, then we obtain almost the same Strichartz estimates as those for the Schrödinger equation associated to a Riemannian metric of dimension 2d ? v.