Self-association of adenine-dependent hairpin ribozymes

Hairpin ribozymes are flexible molecules that catalyse reversible self-cleavage after the docking of two independently folded internal loops, A and B. The activities, self-association and structures in solution of two 85 base adenine-dependent hairpin ribozymes (ADHR1 and ADHR2) were studied by native gel electrophoresis, analytical centrifugation, and small angle neutron scattering. Bi-molecular RNA interactions such as linear–linear, loop–loop, loop–linear or kissing interactions have been found to be important in the control of various biological functions, and hairpin loops present rich potential for establishing both intra- and intermolecular interactions through standard Watson-Crick base pairing or non-canonical interactions. Similar results were obtained for ADHR1 and ADHR2. At room temperature, they indicated end-to-end self-association of the ribozymes in rod-like structures with a cross-section corresponding to two double strands side-by-side. Dimers, which predominate at low concentration (∼0.1 mg/ml), associate into longer rods, with increasing concentration (∼1 mg/ml). Above 65°C, the dimers and rods dissociated into compact monomers, with a radius of gyration similar to that of tRNA (about 70 bases). The dimers were non-active for catalysis, which suggests that dimer formation, probably by preventing the correct docking of loops A and B, could act as an inhibition mechanism for the regulation of hairpin ribozyme catalysis.     

UV light-induced DNA damage detection in the unicellular green alga <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis>

Exposure of cells to ultraviolet radiation (UVR) is one of the best studied and most used model system for the examination of the biological effects of DNA damage, its repair and tolerance. The major product after UVR treatment is cyclobutane pyrimidine dimer (TT, TC, CC). Pyrimidine dimers are repaired by a direct reversal called photoreactivation or by excision of damage in a process of nucleotide excision repair. Several methods have been developed for the detection and quantification of pyrimidine dimers in DNA. The technique of Small and Greimann, in which DNA is incubated with the pyrimidine dimer-specific endonuclease, was used for the analysis of mutant strains with impaired excision repair system of the unicellular green alga Chlamydomonas reinhardtii. Another method is based on the binding of specific monoclonal antibodies to pyrimidine dimers. The aim of our work was to compare these two techniques with the use of mutant strains of C. reinhardtii — uvsX1 and uvsX2 which are assumed to be deficient in DNA damage recognition. One of their traits was sensitivity to UVR which could be caused by breakdown of the excision repair pathway. The results suggest that the immuno-approach is suitable for the detection of DNA damage induced by UVR. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

On the aggregation of bilirubinoids in solution as evidenced by VCD and ECD spectroscopy and DFT calculations

Vibrational and electronic circular dichroism (VCD and ECD) spectra of 3 optically active bilirubin analogs with propionic acid groups replaced by (1) 1‐(S)‐methylpropyl groups, (2) 3‐acetoxy‐1‐(S)‐methylpropyl groups, and (3) 1‐(S)‐2‐(R)‐dimethyl‐2‐(methoxycarbonyl)ethyl groups have been recorded at different concentrations in chloroform. The aliphatic chains attached to C‐8 and C‐12 of the 3 chosen mesobilirubins were modified so as to possess no OH group. The variation of the VCD spectra with concentration is consistent with the formation of dimers at high concentration. Density functional theory and time‐dependent density functional theory calculations on monomeric and dimeric forms support such a conclusion. Comparing with previous VCD (ECD) and IR (UV) studies of other mesobilirubin molecules, it is concluded that here, the key feature for aggregation is the missing OH groups on the propionic acid chains. The latter, in synergy with the polar groups of lactam moieties, appear to be involved in intramolecular phenomena and thus favor monomeric forms. Investigation of ECD and UV spectra of the same compounds in mixed DMSO/chloroform solutions provide further clues to the proposed picture.     

DNA DAMAGE AND PHOTOSYNTHETIC PERFORMANCE IN THE ANTARCTIC TERRESTRIAL ALGA PRASIOLA CRISPA SSP. ANTARCTICA (CHLOROPHYTA) UNDER MANIPULATED UV-B RADIATION

The effect of reduced, natural ambient, and enhanced UV-B radiation (UVBR) on photosynthesis and DNA damage in the Antarctic terrestrial alga Prasiola crispa ssp. antarctica (Kützing) Knebel was investigated in two field experiments. Samples of P. crispa were collected underneath snow cover and exposed outside to reduced and natural UVBR in the austral spring. In a second experiment at the end of the austral summer, samples were exposed to ambient and enhanced UVBR. PSII efficiency, net photosynthetic rate (NP), dark respiration rate (DR), UV-absorbing pigments, and cyclobutyl pyrimidine dimer (CPD) formation were measured during the experiments. In October 1998, a spring midday maximum of 2.0 W·m ^{− 2} of UVBR did not significantly affect effective quantum yield (ΔF/F_m′), and a reduction in the ratio of variable to maximal fluorescence (F_v/F_m) in the late afternoon was transient. Exposure to natural ambient UVBR in October increased CPD values significantly. Midday maxima of UVBR during the experiments in October and January were comparable, but Setlow-DNA-weighted UVBR was more than 50% lower in January than in October. In January, 0.5 W·m ^{− 2} additional UVBR during 10 h did not have a negative effect on ΔF/F_m′. The reduction in F_v/F_m was not significant. NP and DR were not affected by supplementation of UVBR. Although photosynthetic activity remained largely unaffected by UVBR treatment, DNA damage was shown to be a sensitive parameter to monitor UVBR effects. Supplementation of additional UVBR did significantly enhance the amounts of CPD in exposed samples and repair took place overnight. It is concluded that PSII and whole-chain photosynthesis of P. crispa is well adapted to ambient and enhanced levels of UVBR but that CPD formation is more sensitive to UVBR than to photosynthesis.     

Parallel and antiparallel dimers of magainin 2: their interaction with phospholipid membrane and antibacterial activity.

Magainin 2 (M2) forms pores by associating with several other M2 molecules in lipid membranes and shows antibacterial activity. To examine the effect of M2 dimerization on biological activity and membrane interaction, parallel and antiparallel M2 dimers were prepared from two monomeric precursors. Antibacterial and haemolytic activities were enhanced by dimerization. CD measurements showed that both dimers and monomers have an alpha-helical structure in the presence of lipid vesicles. Tryptophan fluorescence shift and KI quenching studies showed that all the peptides were more deeply embedded in acidic liposomes than in neutral liposomes. Experiments on dye-leakage activity and membrane translocation of peptides suggest that dimers and monomers form pores through lipid membranes, although the pore formation may be accompanied by membrane disturbance. Although dimerization of M2 increased the interaction activity with lipid membranes, no appreciable difference between the activities of parallel and antiparallel M2 dimers was observed.     

1,2,4-triazolo[4,3-a]pyrimidines: a new kind of ligands. Structure of the silver(I) dimer with the 7-oxo derivative

This paper describes the silver dinuclear complex [Ag₂L₂(NO₃)₂] · 2H₂O, where L represents the bridging ligand 7,8-dihydro-7-oxo-1,2,4-triazolo[4,3-a]pyrimidine, this being the first example of a coordination compound of a 1,2,4-triazolo[4,3-a]pyrimidine derivative. As a difference with the most studied 1,2,4-triazolo[1,5-a]pyrimidine derivatives, the coordination takes place through the contiguous nitrogen atoms of the triazole ring, closing a six member Ag₂N₄ core with a higher intermetallic distance, 3.4791(3) Å. Linear coordination of silver is not possible in this geometry, so flat trigonal coordination involving also the nitrate counteranion is found instead.     

Diastereomeric stilbene glucoside dimers from the bark of Norway spruce (Picea abies)

As part of a long-term study of the chemical defenses of Norway spruce (Picea abies) against herbivores and pathogens, a phytochemical survey of the phenolics in the bark was carried out. Eight stilbene glucoside dimers, designated as piceasides A-H (1a-4b), were isolated as four 1:1 mixtures of inseparable diastereomers. Their structures were determined by extensive spectroscopic means including 1D (1H and 13C) and 2D NMR (1H-1H COSY, HSQC, HMBC, ROESY) spectra, and were supported by enzymatic hydrolysis and computational analysis.     

Aromatase inhibitory, radical scavenging, and antioxidant activities of depsidones and diaryl ethers from the endophytic fungus Corynespora cassiicola L36

Isolation of a broth extract of the endophytic fungus Corynespora cassiicola L36 afforded three compounds, corynesidones A (1) and B (3), and corynether A (5), together with a known diaryl ether 7. Compounds 1, 3, 5, and 7 were relatively non-toxic against cancer cells, and inactive toward normal cell line, MRC-5. Corynesidone B (3) exhibited potent radical scavenging activity in the DPPH assay, whose activity was comparable to ascorbic acid. Based on the ORAC assay, compounds 1, 3, 5, and 7 showed potent antioxidant activity. However, the isolated natural substances and their methylated derivatives (1−8) neither inhibited superoxide anion radical formation in the XXO assay nor suppressed TPA-induced superoxide anion generation in HL-60 cell line. Corynesidone A (1) inhibited aromatase activity with an IC₅₀ value of 5.30 μM.     

Biochemical properties of <Emphasis Type="Italic">Bacillus intermedius</Emphasis> subtilisin-like proteinase secreted by a <Emphasis Type="Italic">Bacillus subtilis</Emphasis> recombinant strain in its stationary phase of growth

Biochemical properties of Bacillus intermedius subtilisin-like proteinase (AprBi) secreted by a B. subtilis recombinant strain in the early and late stationary phases of growth have been determined. Protein structure was analyzed and its stability estimated. It was noted that the enzyme corresponding to different phases of bacterial growth retains activity in the presence of reducing and oxidizing agents (C₂H₅OH and H₂O₂). Different effects of bivalent metal ions on activity of two proteinase fractions were found. Calcium ions more efficiently activate proteinase secreted in the late stationary phase. Unlike the first enzyme fraction, the second forms catalytically active dimers.     

Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives

The study presented here aimed at identifying a new class of compounds acting against Leishmania parasites, the causative agent of Leishmaniasis. For this purpose, the thioether derivatives of our in-house library have been evaluated in whole-cell screening assays in order to determine their in vitro activity against Leishmania protozoan. Among them, promising results have been achieved with compound RDS 777 (6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine) (IC_50?=_?29.43?µM), which is able to impair the mechanism of the parasite defence against the reactive oxygen species by inhibiting the trypanothione reductase (TR) with high efficiency (K_i 0.25?±?0.18?µM). The X-ray structure of L. infantum TR in complex with RDS 777 disclosed the mechanism of action of this compound that binds to the catalytic site and engages in hydrogen bonds the residues more involved in the catalysis, namely Glu466', Cys57 and Cys52, thereby inhibiting the trypanothione binding and avoiding its reduction.