Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR

Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (>10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815A>G, SMN1). Results of a pilot study with SMA patients are presented.     

Spectroscopic study of (two-dimensional) molecule-based magnets: [M(II)(TCNE)(NCMe)2][SbF6] (M = Fe, Mn, Ni)

The M-[TCNE] (M = 3d metal; TCNE = tetracyanoethylene) system is one of the most interesting classes of molecule-based magnets, exhibiting a plethora of compositions and structures (inorganic polymer chains, 2D layers, 3D networks, and amorphous solids) with a wide range of magnetic ordering temperatures (up to 400 K). A systematic study of vibrational (both infrared and, for the first time, Raman) properties of the family of new TCNE-based magnets of M(II)(TCNE) (NCMe)(2)[SbF(6)] [M = Mn, Fe, Ni] composition is discussed in conjunction with their magnetic behavior and newly reso-lved crystal structures. The vibrational properties of the isolated TCNE(●-) anion in the paramagnetic Bu(4)N [TCNE(●-)] salt and recently characterized 2D layered magnet Fe(II)(TCNE)(NCMe)(2)[FeCl(4)] are also reported for comparison. Additionally, a linear correlation between ν(C=C) (a(g)) frequency of the TCNE ligand and its formal charge Z (the spin density on the π* orbital), Z = [1571 - ν(C=C) (a(g))]/154.5 [e], is presented. It is shown that monitoring Z by Raman spectroscopy is of great use in providing information that allows understanding the peculiarity of the superexchange interaction in M-[TCNE] magnets and establishing the structure-magnetic properties correlations in this class of magnetic material.     

Measurement of reaction kinetics by a pressure rise method

Decomposition of urea nitrate in an initially evacuated system gave sigmoidal pressurevs. time curves. The experimental kinetic data fit the growing nuclei model with a measured enthalpy of activation of 142±12.5 kJ/mole as compared to 115±11.3 kJ/mole obtained thermogravimetrically. This higher value ofH is explained on the basis of two factors: 1) the inhibitory effect of the product gases and 2) self heating, whose extent increasedH by about 12.5 kJ/mole.

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Zusammenfassung Die Zersetzung von Harnstoffnitrat in einem anfanglich evakuierten System ergab sigmoide Druck-Zeit Kurven. Die kinetischen Versuchsangaben können einem Kernwachstums-Modell einer gemessenen Aktivierungsenthalpie von 142±12,5 kJ/mol angepaßt werden, im Vergleich zu den auf thermogravimetrischen Weg ermittelten Wert von 115±11.3 kJ/Mol. Dieser hohe Wert vonH, wird auf Grund zweier Faktoren erklärt: 1) der Hemmungseffekt der Produktgase und 2) Selbsterhitzung, deren AusmaßH um etwa 12.5 kJ/Mol erhöhte.

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Résumé La décomposition du nitrate d'urée dans un système initialement mis sous vide, donne des courbes sigmoïdales de pression en fonction du temps. Les données cinétiques expérimentales peuvent être ajustées à un modèle de grossissement de germes, avec une enthalpie d'activation mesurée de 142±12.5 kJ/mole, comparée à 115±11.3 kJ/mole obtenue par thermogravimétrie. Cette valeur plus élevée deH s'explique sur la base de deux facteurs: 1) l' effet inhibiteur des gaz produits et 2) phénomène d'autoéchauffement qui augmente la valeur deH d'environ 12.5 kJ/mole.

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. , 142+-12.5 / 115 + 11.3 /, . H : 1) 2) , 12.5 /.

     

C-terminal processing of yeast Spt7 occurs in the absence of functional SAGA complex

Background  

Spt7 is an integral component of the multi-subunit SAGA complex that is required for the expression of ~10% of yeast genes. Two forms of Spt7 have been identified, the second of which is truncated at its C-terminus and found in the SAGA-like (SLIK) complex.     

An Isserlis’ Theorem for Mixed Gaussian Variables: Application to the Auto-Bispectral Density

This work derives a version of Isserlis’ theorem for the specific case of four mixed-Gaussian random variables. The theorem is then used to derive an expression for the auto-bispectral density for quadratically nonlinear systems driven with mixed-Gaussian iid noise. C.C. Olson is a NRC Postdoctoral Research Associate.     

Thermochemistry of Binding of Lead(II) and Cadmium(II) by Saccharides in Aqueous Solution

Solution calorimetry was used to determine enthalpies and stability constants for binding of lead(II) or cadmium(II) by galacturonic acid and several monosaccharides in aqueous solution. New values for enthalpies of solution in water are reported for galacturonic acid and maltose monohydrate. The interaction of water solvent with the reactants is the largest factor in the binding process.     

Halophilic reactions of a stable silylene with chloro and bromocarbons

A number of disilanes have been synthesized from a stable silylene, 1 (N,N'-di-tert-butyl-1,3-diaza-2-silacyclopent-4-en-2-ylidene), and a variety of halocarbons. It is proposed that disilane formation is a result of an initial halophilic interaction between the silylene and halocarbon. Formation of disilanes from 1 and CCl4, 2a, CHCl3, 2b, CH2Cl2, 2c, benzyl chloride, 2d, and bromobenzene, 5, are described here. An X-ray crystal structure of 2b was determined.     

Bending of DNA by asymmetric charge neutralization: all-atom energy simulations

DNA dodecamers of the alternating d(CG).d(CG) sequence with six phosphate groups either charge-neutralized or substituted by neutral methylphosphonates across the major or minor groove have been subjected to energy minimization to determine the conformational effect of the asymmetric elimination of phosphate charge. We report bending angles, directions of bending, and detailed structural characteristics such as groove widths and local base-pair parameters. Our principal results are that charge neutralization on one face of the DNA induces significant bending toward the neutralized face, in agreement with theoretical predictions on a simplified model and experimental data on a similar base-pair sequence, and that the DNA conformation averaged over all stereospecific methylphosphonate substitutions is nearly the same as the conformation produced by charge neutralization of the phosphates. Individual isomers, however, cover a wide range of structures, with the magnitude and direction of overall bending sensitive to the precise stereochemical pattern of neutralization. Our simulation does not explicitly contain counterions, and the results therefore suggest that counterions can influence DNA structure by neutralizing the phosphate charge. These data provide new hints into the molecular mechanisms which underlie the deformations of DNA structure induced by the binding of positively charged proteins and other tightly associated cationic species.     

Conformation-dependent state selectivity in O-O cleavage of ONOONO: an "inorganic cope rearrangement" helps explain the observed negative activation energy in the oxidation of nitric oxide by dioxygen

ONOONO has been proposed as an intermediate in the oxidation of nitric oxide by dioxygen to yield nitrogen dioxide. The O-O bond breaking reactions of this unusual peroxide, and subsequent rearrangements, were evaluated using CBS-QB3 and B3LYP/6-311G hybrid density functional theory. The three stable conformers (cis,cis-, cis,trans-, and trans,trans-ONOONO, based on the O-N-O-O dihedral angles of either approximately 0 degrees or approximately 180 degrees ) are predicted to have very different O-O cleavage barriers: 2.4, 13.0, and 29.8 kcal/mol, respectively. These large differences arise because bond breaking leads to correlation of the nascent NO(2) fragments with either the ground (2)A(1) state or the excited (2)B(2) state of NO(2), depending on the starting ONOONO conformation. A cis-oriented NO(2) fragment correlates with the (2)A(1) state, whereas a trans-oriented NO(2) fragment correlates with the (2)B(2) state. Each NO(2) fragment that correlates with (2)A(1) lowers the O-O homolysis energy by approximately 15 kcal/mol, similar to the approximately 17-25 kcal/mol (2)A(1) --> (2)B(2) energy difference in NO(2). Hence, this provides an unusual example of conformation-dependent electronic state selectivity. The O-O bond homolysis of cis,cis-ONOONO is particularly interesting because it has a very low barrier and arises from the most stable ONOONO conformer, and also due to obvious similarities to the well-known [3,3]-sigmatropic shift of 1,5-hexadiene, i.e., the Cope rearrangement. As an additional proof of our state selectivity postulate, a comparison is also made to breakage of the O-O bond of cis,cis-formyl peroxide, where no significant stabilization of the transition state is available because the (2)A(1) and (2)B(2) states of formyloxy radical are near-degenerate in energy. In the case of trans,trans-ONOONO, the O-O bond breaking transition state is a concerted rearrangement yielding O(2)NNO(2), whereas for cis,cis- and cis,trans-ONOONO, the initially formed NO(2) radical pairs can undergo further rearrangement to yield ONONO(2). It is proposed that previous spectroscopic observations of certain N=O stretching frequencies in argon-matrix-isolated products from the reaction of NO with O(2) (or (18)O(2)) are likely from ONONO(2), not the OONO radical as reported.     

Colloidal dynamics on disordered substrates

Using Langevin simulations, we examine driven colloids interacting with quenched disorder. For weak substrates the colloids form an ordered state and depin elastically. For increasing substrate strength, we find a sharp crossover to inhomogeneous depinning and a substantial increase in the depinning force, analogous to the peak effect in superconductors. The velocity versus driving force curve shows criticality at depinning, with a change in scaling exponent occurring at the order to disorder crossover. Upon application of a sudden pulse of driving force, pronounced transients appear in the disordered regime which are due to the formation of long-lived colloidal flow channels.