Synthesis and molecular modelling of double-functionalised nucleosides with aromatic moieties in the 5'-(S)-position and minor groove interactions in DNA zipper structures

A series of six double-functionalised nucleosides, in which aromatic moieties were inserted into the 5'-(S)-C-position, were synthesised and incorporated into DNA duplexes. The aromatic moieties were thymine-1-yl, phenyl, 1,2,3-triazol-1-yl, 1,2,3-triazol-4-yl, 4-(uracil-5-yl)-1,2,3-triazol-1-yl and 4-phenyl-1,2,3-triazol-1-yl. The DNA duplexes were studied with UV melting curves, CD spectroscopy and molecular modelling. The results showed that the aromatic moieties in some cases interact in the minor groove forming DNA zipper structures. The strongest specific interaction was found between two thymines or between a thymine and a phenyl group in a crossed (-3)-zipper motif (i.e., with two base pairs interspacing the modifications). Modelling revealed that the interaction is aromatic stacking across the minor groove. Also, the extended uracil-triazole moiety demonstrated zipper contacts in the minor groove as well as binding to the floor of the groove.     

Plasma-based processes for surface wettability modification

In this article, we describe a method to create rough features on silicon surfaces by reactive etching of a photoresist layer. The roughness and, consequently, the wettability of the surfaces can be modified by modifying the duration of plasma etching. Hydrophobic materials deposited on the rough silicon surface can be modified until a superhydrophobic behavior is obtained, whereas hydrophilic materials become more hydrophilic. The elaboration technique described herein offers an inexpensive and rapid method for the creation of tunable roughness on silicon surfaces with large areas.     

Kinetics of Stem Elongation in Light-Grown Tomato Plants. Responses to Different Photosynthetically Active Radiation Levels by Wild-Type and aurea Mutant Plants

Abstract— In this research, we measured the short- and long-term, stem elongation responses of wild-type and aurea(au) mutant tomato plants to different photosynthetically active radiation (PAR) levels by using linear voltage transducers. Stem elongation was continuously measured in green tomato plants over 2.75 days, under 12 h light/12 h dark photoperiods or in darkness after a 6 h irradiation period. There is no significant difference in stem elongation between wild-type plants pregrown at either LOO or 400 μmol m^?2 s^?1 and then exposed to 12 h photoperiods. However, in the au mutant there is a very large difference between plants pregrown under 100 or 400 umol m ^?2 s^?1 and then exposed either to 12 h photoperiods or to continuous darkness. Total stem elongation of the wild type appears to be maximal at 100 umol m^?2 s^?1, while that of the au mutant appears to be maximal with PAR 400 umol m^?2 s^?1. Wild-type plants displayed PAR-dependent (in the range 100-800 umol m^?2 s^?1) inhibition of growth both during the day and during the night. In contrast, the au mutant showed a fluence-rate-dependent promotion of growth during the dark periods in the range of 10-400 umol m^?2 s^?1. Large, fast and opposite changes in stem elongation rate at the light/dark and dark/light transitions were present in both genotypes. Internode elongation rate in the first half of the night was always modest in wild-type tomato, whereas it increased rapidly in the au mutant. Stem elongation rate of wild type starts to increase after about 6 h in darkness, showing the typical time course of escape from Pfr-mediated inhibition of elongation by an end-of-day response. The role of phytochrome level and type in sensing light quantity is discussed.     

Synthesis of the C-linked disaccharide alpha-D-Man-(1-->4)-D-Man employing a SmI(2)-mediated C-glycosylation step: en route to cyclic C-oligosaccharides

Investigations are reported on the assembly of the C-linked disaccharide alpha-D-Man-(1-->4)-D-Man, representing the first steps in our projected synthesis of a cyclic C-oligomer containing repeating units of this C-dimer. The key step in this synthesis uses a SmI(2)-mediated coupling of 2,3,4,6-tetra-O-benzyl-alpha-D-mannopyranosyl 2'-pyridyl sulfone with a C4-formyl branched mannopyranoside unit, affording the C-disaccharide derivative with complete stereocontrol at the two new stereogenic centers. Subsequently, a modified tin hydride based deoxygenation produced the target carbohydrate analogue. The synthesis of the C4-formyl monosaccharide makes use of a stereoselective radical-based allylation followed by double bond migration and ozonolysis.     

Search for melanoma markers in plasma and serum samples

Fourteen blood samples from patients with melanoma and eleven blood samples from healthy subjects were analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The study was focussed on species of low molecular weight, in the range 800-5000 Da, present in plasma and sera. While for healthy subjects plasma samples lead to the production of a higher number of ionic species, for melanoma patients a high number of diagnostic ions, present with high frequency and with quite high relative abundance, are present in particular in serum samples and to a lesser extent also in plasma. Since plasma samples are obtained more easily in comparison to sera, it is possible to suggest that also plasma can be used for these studies.     

The Use of UV Radiation to Control the Architecture of Salvia splendens Plants. II. Relationships between PAR Levels and UV Radiation in the Photoregulation of Stem Elongation

The effects of UV irradiation on stem elongation of Salvia splendens plants preadapted to two and grown under four different irradiances of visible light, were studied using linear voltage differential transducers. The levels of radiant energy during the experimental phase showed a temporary and opposite effect during the day-time and the night-time: increasing levels of photosynthetically active radiation (PAR)? reduced stem growth during the day and enhanced elongation growth during the night. It appears, therefore, that similar final stem elongation in plants grown under very different PAR levels is the result of the algebraic sum of different and sometimes opposite effects of PAR on stem growth. Except for the controls, the plants received one UV treatment from Philips TL 12 40 W fluorescent tubes either in the middle of the light period or at the beginning of the dark period. The results show that the preadapting PAR conditions changed the sensitivity of the plants to both UV and to the following PAR conditions. The sensitivity of S. splendens to UV radiation is inversely correlated to the PAR levels before and during the UV treatments. Furthermore the presence of active photosynthetic and photomorphogenic systems, i. e. the presence of visible light during the UV treatment, decreases the sensitivity of the plants to UV radiation. Depending on PAR levels, the UV treatments given during the night induced a temporary inhibition of growth followed by a promotion of stem elongation.     

Detailed structure of hairy mixed micelles formed by phosphatidylcholine and PEGylated phospholipids in aqueous media

Aqueous dispersions of mixed egg yolk phosphatidylcholine (PC) and poly(ethylene glycol) (PEG) modified distearoyl phosphatidylethanolamine (DSPE) were investigated with the purpose of determining shape, size, and conformation of the formed mixed micelles. The samples were prepared at a range of DSPEPEG to PC molar ratios ([DSPEPEG/PC] from 100:0 to 30:70) and with, respectively, DSPEPEG2000 and DSPEPEG5000, where 2000 and 5000 refer to the molar masses of the PEG chains. Particle shape and internal structure were studied using small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The contrast of the micelles is different for X-rays and neutrons, and by combining SANS and SAXS, complementary information about the micelle structure was obtained. The detailed structure of the micelles was determined in a self-consistent way by fitting a model for the micelles to SANS and SAXS data simultaneously. In general, a model for the micelles with a hydrophobic core, surrounded by a dense hydrophilic layer that is again surrounded by a corona of PEG chains in the form of Gaussian random coils attached to the outer surface, is in good agreement with the scattering data. At high DSPEPEG contents, nearly spherical micelles are formed. As the PC content increases the micelles elongate, and at a DSPEPEG/PC ratio of 30:70, rodlike micelles longer than 1000 angstroms are formed. We demonstrate that by mixing DSPEPEG and PC a considerable latitude in controlling the particle shape is obtained. Our results indicate that the PEG chains in the corona are in a relatively unperturbed Gaussian random coil conformation even though the chains are far above the coil-coil overlap concentration and, therefore, interpenetrating. This observation in combination with the observed growth behavior questions that the "mushroom-brush"transition is the single dominating factor for determining the particle shape as assumed in previous theoretical work (Hristova, K.; Needham, D. Macromolecules 1995, 28, 991-1002).     

2'-Spiro ribo- and arabinonucleosides: synthesis, molecular modelling and incorporation into oligodeoxynucleotides

We have synthesized four conformationally restricted bicyclic 2'-spiro nucleosides via 2'-C-allyl nucleosides as key intermediates. The ribo-configured 2'-spironucleosides 9b and 14b were obtained by a convergent strategy starting from 2-ketofuranose 1 whereas the arabino-configured 2'-spironucleosides 21 and 27 were obtained by a linear strategy with a 2'-ketouridine derivative as starting material. The furanose ring of 9b/14b adopts N-type conformations whereas the furanose ring of 21/27 exists as an N<==>S equilibrium. These compounds showed no anti-HIV-1 activity or cytotoxicity. Incorporation of the four 2'-spironucleosides (as monomers X4 and X5) into oligodeoxynucleotides was accomplished using the phosphoramidite approach on an automated DNA synthesizer. Irrespective of monomeric configuration, hybridization studies revealed that these 2'-spironucleotide monomers (X4 and X5) induce decreased duplex thermostabilities compared with the corresponding DNA:DNA and DNA:RNA duplexes. Molecular modelling indicated that steric constraints are a possible reason for the lowered binding affinities of the modified oligodeoxynucleotides towards complementary single-stranded DNA and single-stranded RNA complements.     

Organophosphorus insecticides extraction and heterogeneous oxidation on column for analysis with an acetylcholinesterase (AChE) biosensor

This paper presents an analysis method for organophosphorus insecticides based on AChE biosensors coupled with a preconcentration and oxidation on a solid phase column. Three organic solvents, acetonitrile (ACN), ethanol and methanol were tested for their influence on AChE activity, insecticide inhibition and their ability to elute the adsorbed insecticides. Our results showed that ACN in a concentration of 5% (v/v) had the less negative effect on biosensor analysis and was the most appropriate organic solvent for the column elution. The presence of the organic solvent in the incubation media of the biosensor was found to induce a reduction of the inhibition percentages. The inhibition of the biosensors was performed in phosphate buffer with 5% (v/v) ACN, while the initial and remaining response of the biosensors were measured in PBS. In these conditions, the LODs of paraoxon and dichlorvos were measured with or without a preconcentration step. The LODs of the AChE biosensor without sample preconcentration were 8 × 10⁻⁸ M for paraoxon and 1 × 10⁻⁷ M dichlorvos and the LOD obtained after the preconcentration step were 2.5 × 10⁻⁸ M for paraoxon and 2.5 × 10⁻⁸ M for dichlorvos. Moreover, the use of the column allowed the heterogeneous oxidation of organophosphorus insecticides for improved LOD.