Spectroscopic and photophysical properties of dUTP and internally DNA bound fluorophores for optimized signal detection in biological formats

Efficient signal generation in DNA-based assays requires understanding of the influence of fluorophore's interactions on the spectroscopic properties. The resulting changes in fluorescence intensity, quantum yield, emission anisotropy, and fluorescence lifetime provide straightforward tools for the study of molecular dynamics and interaction between labels and nucleic acids. Searching for bright fluorescent reporters for rolling circle amplification (RCA) as efficient signal enhancement strategy for biological formats, we investigated the spectroscopic properties of seven dyes: cyanines, rhodamines, and BODIPYs. They spectrally resemble Cy3, the most frequently used fluorophore in biodetection formats, and are measured in six samples (free dye, dye-dUTP, internally labeled ssDNA and dsDNA-single- and triple-labeled) using steady-state and time-resolved fluorometry. Special emphasis was dedicated to characterizing the nature of the interaction of these fluorophores differing in dye class, charge, and rigidity. Our results suggest dye charge and structure as main factors governing the dye's interactions, with DY-555 and Cy3B presenting the best candidates for our envisaged signal amplification strategy. This label comparison underlines the importance of a proper understanding of structure-property relations and dye-biomolecule interactions for reporter choice and presents a road map towards the design and interpretation of experiments using these labels on DNA of known sequence.     

A Survey of Information Entropy Metrics for Complex Networks

Information entropy metrics have been applied to a wide range of problems that were abstracted as complex networks. This growing body of research is scattered in multiple disciplines, which makes it difficult to identify available metrics and understand the context in which they are applicable. In this work, a narrative literature review of information entropy metrics for complex networks is conducted following the PRISMA guidelines. Existing entropy metrics are classified according to three different criteria: whether the metric provides a property of the graph or a graph component (such as the nodes), the chosen probability distribution, and the types of complex networks to which the metrics are applicable. Consequently, this work identifies the areas in need for further development aiming to guide future research efforts.     

Density functional theory study of the oxidation reaction in the gas and aqueous phase of allyl methyl disulfide with hydroxyl radical

Structural Chemistry - An in silico analysis of the oxidation mechanism of allyl methyl disulfide (AMDS) by hydroxyl radical was achieved at DFT level using B3LYP, CAM-B3LYP, M06-2X, and BMK...     

Effect of isotopic mass on the photoluminescence spectra of β zinc sulfide

Zinc sulfide is a wide bandgap semiconductor which crystallizes in either the wurtzite modification (α-ZnS), the zincblende modification (β-ZnS) or as one of several similar tetrahedrally coordinated polytypes. In this work, we report a photoluminescence study of different samples of isotopically pure β-ZnS crystals, and crystals with the natural isotopic abundances, at 15 and 77 K. The derivatives of the free and bound exciton energies on isotopic mass have been obtained. They allow us to estimate the contribution of the zinc and sulfur vibrations to the bandgap renormalization energy by electron-phonon interaction. A two-oscillator model based on the zinc and sulfur renormalization energies has been used to account for the temperature dependence of the bandgap energy in ZnS. The results are compared with those found for other tetrahedrally coordinated semiconductors.     

Multiple immunoblot: a sensitive technique to stain proteins and detect multiple antigens on a single two-dimensional replica

A multiple immunoblotting technique was developed to positively identify up to three different antigens on a single nitrocellulose replica of a two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel. Three highly sensitive immunoblot assays were selected, including: horseradish peroxidase/luminescence, alkaline phosphatase, and silver-enhanced immunogold. As a major advantage, the method permits a simultaneous detection of up to three different antigens without eluting the antibody-dye complex between staining of single polypeptides, thus providing a highly accurate identification of closely migrating components. The staining procedure is summarized in a flow chart. In addition to the multiple immunoblot staining, some suggestions are provided for a sensitive protein staining.     

Beiträge zur Kenntnis der Hydratationsvorgänge beim Abbinden des Portlandzements und des Klinkers

Ohne Zusammenfassung Hans Pulfrich, Beitr?ge zur Kenntnis der Hydratationsvorg?nge beim Abbinden des Portlandzements, Inaug.-Diss. (Jena 1922). Unver?ffentlicht.     

Ueber die Hydratation natürlicher und künstlicher Gläser

Ohne Zusammenfassung Gerhart Schott, Ueber die Hydratation natürlicher und künstlicher Gesteinsgl?ser. Inaug.-Diss. (Jena 1923). Unver?ffentlicht.     

Computational study of the hydrogen peroxide scavenging mechanism of allyl methyl disulfide,an antioxidant compound from garlic

Molecular Diversity - Although many sulfur containing garlic compounds present antioxidant activity, little is known about molecular mechanisms through which these compounds react with reactive...     

Testing the Pauli exclusion principle with the NEMO-2 detector

The Pauli Exclusion Principle (PEP) was tested with the NEMO-2 detector. Limits at the 90% C.L. on the violation of PEP for p-shell nucleons in ¹²C were obtained. Specifically, transitions to the fully occupied 1s _1/2-shell yielded a limit of 4.2 · 10²⁴ y for the process with emission of a γ-quantum. Similarly limits of 3.1 · 10²⁴ y for β⁻ and 2.6 · 10²⁴ y for β⁺ Pauli-forbidden transitions of ¹²C →¹²?¹²B) are reported here. Received: 25 August 1999     

Theoretical study of the highly diastereoselective 1,3-dipolar cycloaddition of 1,4-dihydropyridine-containing azomethine ylides to [60]fullerene (Prato's reaction)

The 1,3-dipolar cycloaddition of azomethine ylides bearing the biologically active 1,4-dihydropiridine ring to C(60) was investigated by means of quantum mechanical calculations at the semiempirical AM1 and DFT (B3LYP/6-31G) methods. The presence of two chiral centers and one chiral axis in the resulting fulleropyrrolidines leads to four possible [6,6] cycloaddition products. Formation of atropoisomers has also been considered. The transition-state structures were computed for the four different cycloaddition pathways to find out the lowest activation energy stereoisomer. In all cases, a frequency analysis and an IRC calculation were carried out to fully characterize the located transition-state structures. AM1 results and single-point energy calculations at the B3LYP/6-31G//AM1 level for the four transition-state structures yield activation energies values below 5 kcal/mol.