Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set

We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis and biotechnological applications.     

Investigation of spacer influences in phosphorescent‐emitting nonconjugated PLED systems

An assay was introduced to clarify influences on electroluminescent behavior for RGB‐colored phosphorescent terpolymers with N,N‐Di‐p‐tolyl‐aniline as hole‐transporting unit, 2‐(4‐biphenyl)‐5‐(4‐tert‐butylphenyl)‐1,3,4‐oxadiazole (tert‐BuPBD) as electron‐transporting unit, and different iridium complexes in RGB‐colors as triplet emitting materials. All monomers were attached with spacer moieties to the “para” position of a polystyrene. Polymer light emitting diodes (PLEDs) were built to study the electro‐optical behavior of these materials. The gist was a remarkable influence of hexyl‐spacer units to the PLED performance. For all three colors only very restricted PLED performances were found. In comparison RGB‐terpolymers were synthesized with directly attached charge transport materials to the polymer backbone. For this directly linked systems efficiencies were 28 cd A^?1 @ 6 V (green), 4.9 cd A^?1 @ 5 V (red) and 4.3 cd A^?1 @ 6 V (bluish). In summary we assume that an improved charge percolation pathways regarding to the higher content of semiconducting molecules and an improved charge transfer to the phosphorescent dopand in the case of the copolymers without spacers are responsible for the better device performance comparing the copolymers with hexyl spacers. The approach of the directly connected charge transport materials at the nonconjugated styrene polymer backbone should be favored for further investigations, therefore. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 389–402, 2010     

Saccharide-modified nanodiamond conjugates for the efficient detection and removal of pathogenic bacteria

The detection and removal of bacteria, such as E. coli in aqueous environments by using safe and readily available means is of high importance. Here we report on the synthesis of nanodiamonds (ND) covalently modified with specific carbohydrates (glyco-ND) for the precipitation of type 1 fimbriated uropathogenic E. coli in solution by mechanically stable agglutination. The surface of the diamond nanoparticles was modified by using a Diels-Alder reaction followed by the covalent grafting of the respective glycosides. The resulting glyco-ND samples are fully dispersible in aqueous media and show a surface loading of typically 0.1 mmol g(-1). To probe the adhesive properties of various ND samples we have developed a new sandwich assay employing layers of two bacterial strains in an array format. Agglutination experiments in solution were used to distinguish unspecific interactions of glyco-ND with bacteria from specific ones. Two types of precipitates in solution were observed and characterized in detail by light and electron microscopy. Only by specific interactions mechanically stable agglutinates were formed. Bacteria could be removed from water by filtration of these stable agglutinates through 10 μm pore-size filters and the ND conjugate could eventually be recovered by addition of the appropriate carbohydrate. The application of glycosylated ND allows versatile and facile detection of bacteria and their efficient removal by using an environmentally and biomedically benign material.     

Structure and function of proteins in hydrated choline dihydrogen phosphate ionic liquid

Ionic liquids are being intensely studied as promising media for the stabilization of proteins and other biomolecules. Choline dihydrogen phosphate (CDHP) has been identified as one of the most promising candidates for this application. In this work we have probed in more detail the effects that CDHP may have on the thermodynamics, structure, and stability of proteins, including one of therapeutic interest. Microcalorimetry and circular dichroism spectropolarimetry (CD) were used to assess the thermal stability of protein solutions in CDHP/water mixtures at various concentrations. Increasing thermal stability of lysozyme and interleukin-2 in proportion to CDHP concentration was observed. Isothermal titration calorimetry (ITC) was used to quantify binding interactions, and indicate that the mechanism for stability does not appear to be dependent upon CDHP binding to protein. CD and small angle X-ray scattering (SAXS) analyses were used to probe for structural changes due to the presence of CDHP. SAXS indicates charge effects on the surface of the protein play a role in protein stability in ionic liquids, and no significant alteration of the overall tertiary conformation of lysozyme was observed at 25 °C. However, after incubation at 37 °C or at higher concentrations of CDHP, small changes in protein structure were seen. Effects on protein activity were monitored using turbidity assays, and CDHP decreases protein activity but does not eliminate it. Protein solubility was also monitored using a turbidity assay and was found to be inversely proportional to the concentration of CDHP in solution.     

Radin forcing and its iterations

We provide an exposition of supercompact Radin forcing and present several methods for iterating Radin forcing. This work was partially supported by FWF project number P16790-N04.     

A General Label Search to investigate classical graph search algorithms

Many graph search algorithms use a labeling of the vertices to compute an ordering of the vertices. We generalize this idea by devising a general vertex labeling algorithmic process called General Label Search (GLS), which uses a labeling structure which, when specified, defines specific algorithms.We characterize the vertex orderings computable by the basic types of searches in terms of properties of their associated labeling structures. We then consider performing graph searches in the complement without computing it, and provide characterizations for some searches, but show that for some searches such as the basic Depth-First Search, no algorithm of the GLS family can exactly find all the orderings of the complement. Finally, we present some implementations and complexity results of GLS on a graph and on its complement.     

Cognitive resource allocation for neural activity underlying mathematical cognition: a multi-method study

Mathematical cognition requires the allocation of computation resources, where math-specific computations are assumed to take place in the parietal cortex and math-supportive computations in the frontal cortex. Because the pupil dilation has a higher temporal resolution than functional MRI (fMRI), the study investigated to which extent the pupil dilation can help to identify cognitive resource allocation for neural activity underlying math-specific and math-supportive cognition. Combining pupillometry and event-related fMRI, we administered a multiplication verification paradigm to 15 healthy participants asking them to solve easy, moderate, and difficult multiplication tasks. The results revealed that (1) behavioral and pupil dilation data increased parametrically with task difficulty; (2) mental multiplication with increasing difficulty recruited a fronto-parietal circuit comprising left pre-supplementary motor area, left precentral gyrus, right dorsolateral prefrontal cortex, and bilateral intraparietal sulcus (IPS); and (3) pupil dilation was sensitive to cognitive resource allocation for neural activity underlying math-specific cognition in the bilateral IPS, implicating a strong reliance on numerical quantity processing during multiplication. In conclusion, the pupil dilation could be used in mathematics education as an easily acquired peripheral physiological indicator (without relying on fMRI) that might lead to a better understanding of dynamical changes in learning arithmetic abilities as a function of training, experience, and development. On a broader level, its application allows to obtain useful insights into learning disabilities such as dyscalculia, and further improve rehabilitation programs with appropriate intervention structures.