A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability

Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K⁺ or Sr²⁺. TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.     

Carboxyl groups in pre-treated regenerated cellulose fibres

The influence of peroxide bleaching and slack-mercerization on the amount of acidic groups in regenerated fibres (viscose, modal and lyocell) were studied. Conductometric titration was used to determine the total content of acidic carboxylic groups. Polyelectrolyte titration was used for surface and total charge determination, and to obtain information about the charge distribution and accessibilities of charged groups. Changes in fibre crystallinity to pre-treatment processes were characterized using iodine sorption (Schwertassek method) and correlated to treatments and the amount of carboxylic groups. For all three types of fibres the amount of accessible carboxyl groups was lowered by an increase in the degree of crystallinity. Bleaching with hydrogen peroxide causes some oxidative cellulose damage and, therefore, a larger amount of carboxyl groups (presumably formed at the end of cellulose chains). Slack-mercerization did not significantly change the total amount of acidic groups in the fibres, but their accessibility to cationic polyelectrolytes, in particular to polymers with high molecular weight was substantially lowered. Lidija Fras Zemljič, Zdenka Peršin, and Karin Stana Kleinschek are the members of the European Polysaccharide Network of Excellence (EPNOE).     

Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611

An important class of red fluorescent proteins (RFPs) feature a 2-iminomethyl-5-(4-hydroxybenzylidene)imidazolinone chromophore. Among these proteins, eqFP611 has the chromophore in a coplanar trans orientation, whereas the cis isomer is preferred by other RFPs such as DsRed and its variants. In the photoactivatable protein asFP595, the chromophore can even be switched from the nonfluorescent trans to the fluorescent cis state by light. By using X-ray crystallography, we have determined the structure of dimeric eqFP611 at high resolution (up to 1.1 A). In the far-red emitting eqFP611 variant d2RFP630, which carries an additional Asn143Ser mutation, the chromophore resides predominantly (approximately 80%) in the cis isomeric state, and in RFP639, which has Asn143Ser and Ser158Cys mutations, the chromophore is found completely in the cis form. The pronounced red shift of excitation and emission maxima of RFP639 can thus unambiguously be assigned to trans-cis isomerization of the chromophore. Among RFPs, eqFP611 is thus unique because its chromophore is highly fluorescent in both the cis and trans isomeric forms.     

Porphyrin complexes containing coordinated BOB groups: synthesis, chemical reactivity and the structure of [BOB(tpClpp)]2+

The reactions of boron halides with free base porphyrins under conditions where partial hydrolysis of the boron halides can occur give diboron porphyrin complexes containing BOB moieties in which each boron is bonded to two porphyrin nitrogen atoms. BF(3).OEt(2) with H(2)(por) gives B(2)OF(2)(por) (por = tpp, ttp, tpClpp, oep) which has an asymmetric structure in which one boron lies in the porphyrin plane (B(ip)) while the other lies above it (B(oop)). BCl(3).MeCN with H(2)(por) gives B(2)O(2)(BCl(3))(2)(por) which contains a four-membered B(2)O(2) ring and is stable only in the presence of excess BCl(3). BBr(3) with Li(2)(tpClpp) gives the dicationic complex [B(2)O(tpClpp)](2+) as its [BBr(4)](-) salt, and is the first example of a boron porphyrin containing three-coordinate boron to be structurally characterised. B(2)O(2)(BCl(3))(2)(por) can be chromatographed on basic alumina to give the hydroxyboron complex B(2)O(OH)(2)(por), which is deduced from its NMR spectra and DFT calculations to have a structure analogous to B(2)OF(2)(por). The OH protons are shifted upfield to near delta -4 (B(oop)-OH) and -10 (B(ip)-OH) by the diamagnetic porphyrin ring current. The reaction of either B(2)O(2)(BCl(3))(2)(por) or B(2)O(OH)(2)(por) (por = ttp, tpClpp) with alcohols (ROH, R = Et, 4-C(6)H(4)CH(3)) gives B(2)O(OR)(2)(por), which can in turn be converted to B(2)O(OR)(OH)(por) by repeated chromatography. The reaction of PhBCl(2) with H(2)(por) (por = ttp, tpClpp) gives B(2)O(Ph)(OH)(por) which has been characterised by spectroscopy in concert with DFT calculations. It is a further example of the B(2)OF(2)(por) structural type, in which the phenyl group is coordinated to the out-of-plane boron and the OH group to the in-plane boron, as are its derivatives B(2)O(Ph)(X)(tpClpp) (X = F, OEt). Steric drivers for the facile hydrolysis of haloboron porphyrins relative to their dipyrromethene and expanded porphyrin counterparts are discussed.     

226Ra translocation from soil to selected vegetation in the Crucea (Romania) uranium mining area

A two year field survey of ²²⁶Ra translocation from soil to selected spontaneous plants growing in the Crucea (Romania) uranium mining area is presented. Since Crucea is a large and relatively highly contaminated area, an easy and cheap way for a desired lowering of radiopollution represents phytoremediation using plentifully occurring plant species. The ²²⁶Ra translocation from soil was affected by analyzed species, collecting sites and vegetation periods. The specific ²²⁶Ra activities of the roots were considerably higher than the aboveground parts confirming the root tropism of radioisotopes. Mentha piperita was found to be highly effective in phytoremediation, especially in autumn.     

Effect of CyDye minimum labeling in differential gel electrophoresis on the reliability of protein identification

Differential 2-DE (DIGE) is a widely applied tool for the quantitative analysis of differentially represented proteins. The method involves covalent minimal labeling of proteins prior to their electrophoretic separation using CyDye DIGE Fluor minimal dyes. This methodology creates two different species per protein, the labeled (approx. 1-2%) and unlabeled (approx. 98-99%) ones, which differ in their molecular masses by 434-464 Da, depending on the attached dye. DIGE followed by automated spot picking according to the CyDye coordinates misses in many instances the exact positions where the maximum amounts of the considered proteins are located. This fact leads to a loss in sensitivity of the subsequent MALDI-MS analyses and results in a reduced reliability of protein identification and sequence coverage. In this paper, the migration differences of labeled and unlabeled species are quantified together with the impact of this effect on the certainty of protein identification and sequence coverage investigating proteins up to 90 kDa.     

Studies on Immobilization and Partial Characterization of Lipases from Wheat Seeds (<Emphasis Type="Italic">Triticum aestivum</Emphasis>)

The objective of this study was to provide some features on immobilization and partial characterization of lipases from wheat seeds. The optimum pH and temperature were found to be 5.5 and 32–37 °C, respectively. The stability of the concentrated enzymatic extract to high temperatures (25, 35, 45, and 55 °C) showed that the incubation of the extract at 55 °C led to its complete inactivation. The concentrated enzymatic extract kept 90% of its hydrolytic and esterification activities until 70 and 40 days of storage at 4 °C, respectively. The extract presented higher hydrolytic specificity to substrates of medium and long chains and higher esterification affinity to fatty acids of short and medium chains and alcohols with two and three carbon atoms. After the immobilization process using activated coal and sodium alginate as supports, an enhancement of about threefold in lipase activity was observed. The development of the present work permitted us to point out some characteristics of lipases from wheat seeds necessary for the proposition of new future industrial applications for this important biocatalyst.     

Biomimetic membrane arrays on cast hydrogel supports

Lipid bilayers are intrinsically fragile and require mechanical support in technical applications based on biomimetic membranes. Tethering the lipid bilayer membranes to solid substrates, either directly through covalent or ionic substrate-lipid links or indirectly on substrate-supported cushions, provides mechanical support but at the cost of small molecule transport through the membrane-support sandwich. To stabilize biomimetic membranes while allowing transport through a membrane-support sandwich, we have investigated the feasibility of using an ethylene tetrafluoroethylene (ETFE)/hydrogel sandwich as the support. The sandwich is realized as a perforated surface-treated ETFE film onto which a hydrogel composite support structure is cast. We report a simple method to prepare arrays of lipid bilayer membranes with low intrinsic electrical conductance on the highly permeable, self-supporting ETFE/hydrogel sandwiches. We demonstrate how the ETFE/hydrogel sandwich support promotes rapid self-thinning of lipid bilayers suitable for hosting membrane-spanning proteins.     

Dissolvable disulphide-polyacrylamide gels for the electrophoretic analysis of chromosomal proteins and for affino-electrophoresis of thiol-proteins

A discontinous gel system is described that is composed of the dissolvable, disulphide-containing acrylamide gel developed by Hansen and the acetic acid-urea gel as introduced by Panyim and Chalkley. A cleavable SDS gel is used for the identification and an initial separation of proteins according to molecular weight; it is then solubilized by tris-mercaptoethanol and layered on the acidic gel, where it functions as a stacking gel with a pronounced concentrating capacity. The final resolution obtained by this technique permits the identification of single protein species according to the degree of enzymatic modification (acetylation and phosphorylation). Side reactions of the disulphide gel matrix with thiol proteins are discussed and other possible application are considered.     

Additional Isoquinoline Alkaloids from Lltsea Cubeba

By combination of centrifugal partition chromatography (CPC) and common separation methods, seven additional known bases were isolated and characterized from the reinvestigation of L. cubeba besides three previously isolated bases- isocorydine (10), N-methyllaurotetanine (9), and boldine (2). They are laurolitsine (1), laurotetanine (3), isoboldine (4), norisocorydine (5), N-methyllindcarpine (7), isodomesticine (8), and glaziovine (6). Among these, compound 9 is the most abundant (7.5 × 10^?4) and will be modified for pharmacological tests. This work will be of value for chemotaxonomy.