Speeding up biomolecular interactions by molecular sledding

Numerous biological processes involve association of a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Similarly, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.     

Wikipedia ranking of world universities

We use the directed networks between articles of 24 Wikipedia language editions forproducing the wikipedia ranking of world Universities (WRWU) using PageRank, 2DRank andCheiRank algorithms. This approach allows to incorporate various cultural views on worlduniversities using the mathematical statistical analysis independent of culturalpreferences. The Wikipedia ranking of top 100 universities provides about 60% overlap withthe Shanghai university ranking demonstrating the reliable features of this approach. Atthe same time WRWU incorporates all knowledge accumulated at 24 Wikipedia editions givingstronger highlights for historically important universities leading to a differentestimation of efficiency of world countries in university education. The historicaldevelopment of university ranking is analyzed during ten centuries of their history.     

Synthesis, ionisation potentials and electron affinities of hexaazatrinaphthylene derivatives

Several hexaazatrinaphthylene derivatives and a tris(thieno)hexaazatriphenylene derivative have been synthesised by reaction of the appropriate diamines with hexaketocyclohexane. The crystal structure of 2,3,8,9,14,15-hexachloro-5,6,11,12,17,18-hexaazatrinaphthylene has been determined by X-ray diffraction; this reveals a molecular structure in good agreement with that predicted by density functional theory (DFT) calculations and pi-stacking with an average spacing between adjacent molecular planes of 3.18 A. Solid-state ionisation potentials have been measured by using UV photoelectron spectroscopy and fall in the range of 5.99 to 7.76 eV, whereas solid-state electron affinities, measured using inverse photoelectron spectroscopy, vary in the range -2.65 to -4.59 eV. The most easily reduced example is a tris(thieno)hexaazatriphenylene substituted with bis(trifluoromethyl)phenyl groups; DFT calculations suggest that the highly exothermic electron affinity is due both to the replacement of the outermost phenylene rings of hexaazatrinaphthylene with thieno groups and to the presence of electron-withdrawing bis(trifluoromethyl)phenyl groups. The rather exothermic electron affinities, the potential for adopting pi-stacked structures and the low intramolecular reorganisation energies obtained by DFT calculations suggest that some of these molecules may be useful electron-transport materials.     

Photoabsorption and photofragmentation of isolated cationic silver cluster-tryptophan hybrid systems

We present a theoretical study of the size and structure selective absorption properties of cationic silver cluster-tryptophan Trp-Ag(n)(+) (n = 2-5,9) hybrid systems supported by photofragmentation experiments. Our time-dependent density functional theory calculations provide insight into the nature of excitations in interacting nanoparticle-biomolecule subunits and allow to determine characteristic spectral features as fingerprints of two different classes of structures: charge solvated and zwitterionic. Moreover, different types of charge transfer transitions have been identified. Charge transfer from pi system of tryptophan to silver cluster occurs for charge solvated structures while charge transfer from silver to the NH(3) (+) group takes place for zwitterionic structures. This has been confirmed by experimentally measured photofragmentation channels and molecular dynamics simulations. Our findings provide fundamental insight into the structure- and size-dependent mechanism responsible for the enhanced absorption and emission in nanoparticle-biomolecular hybrid systems.     

An efficient synthesis of enantiomerically pure (R)-pipecolic acid, (S)-proline, and their N-alkylated derivatives

Enantiomerically pure (R)-(+)-pipecolic acid was synthesized in four steps and 42% overall yield starting from dihydropyran and (R)-alpha-methylbenzylamine. A general short strategy is also described for preparing (S)-proline (47.5% overall yield) and derivatives.     

Simultaneous temperature and 2D velocity measurements in a turbulent heated jet using combined laser-induced fluorescence and LDA

 This paper presents an efficient technique for the characterization of thermal transport properties in turbulent flows. The method is based on the temperature dependence of fluorescence, induced by laser radiation, of an organic dye. The laser-induced fluorescence technique is combined with 2D laser Doppler anemometry, in order to measure in the same sample volume simultaneously and instantaneously the temperature and velocity. The technique is demonstrated on a turbulent heated round jet: the mean and fluctuating dynamic and thermal fields are investigated, and the temperature-velocity cross-correlations are determined in order to characterize the turbulent diffusivity and the turbulent Prandtl number. Received: 30 October 1997/Accepted: 14 July 1998