Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

Vibrational spectroscopy of aqueous solutions at high concentrations: Raman and inelastic neutron scattering

We review work performed by our group on vibrational spectroscopy of water and aqueous solutions of strong II-I electrolytes at high concentrations. Evidence shall be presented for the existence of intermediate range, solute-connected, ordered patches, whose collective vibrational modes yield a continuous vibrational density of states, as in amorphous solids. We shall review Raman and inelastic neutron scattering results, obtained for electrolytes such as ZnCl₂, NiCl₂, CuBr₂, CdCl₂. Other results, such as EXAFS, viscosity and ultrasonic attenuation will also be discussed.     

Axial dispersion in a liquid fluidized bed of particles akin to immobilized enzymes

The axial dispersion of a liquid fluidized bed of controlled pore silica (CPS) particles has been determined by the pulse tracer method. The CPS used was the same as for enzyme immobilization, having an average diameter of 0.436 mm and mean pore size of 37.5 nm. The fluidization liquid is α-amylase liquefied manioc starch, 30% w/v, 45°C pH=4.5. Nominal bed porosities tested were 0.7 and 0.8. The results show that the axial dispersion coefficient increases with greater superficial liquid velocities. Various available correlations tested disagree with each other to a large extent and are unable to represent collected experimental data.     

Characterization of Sol-gel bioencapsulates for ester hydrolysis and synthesis

Candida rugosa lipase was entrapped in silica sol-gel particles prepared by hydrolysis of methyltrimethoxysilane and assayed by p-nitrophenyl palmitate hydrolysis, as a function of pH and temperature, giving pH optima of 7.8 (free enzyme) and 5.0–8.0 (immobilized enzyme). The optimum temperature for the immobilized enzyme (50–55°C) was 19°C higher than for the free enzyme. Thermal, operational, and storage stability were determined with n-butanol and bytyric acid, giving at 45°C a half-life 2.7 times greater for the immobilized enzyme; storage time was 21 d at room temperature. For ester synthesis, the optimum temperature was 47°C, and high esterification conversions were obtained under repeated batch cycles (half-life of 138 h).     

Metal ion catalysis in the beta-elimination reactions of N-[2-(4-pyridyl)ethyl]quinuclidinium and N-[2-(2-pyridyl)ethyl]quinuclidinium in aqueous solution

Catalysis of the beta-elimination reaction of N-[2-(4-pyridyl)ethyl]quinuclidinium (1) and N-[2-(2-pyridyl)ethyl]quinuclidinium (2) by Zn(2+) and Cd(2+) in OH(-)/H(2)O (pH = 5.20-6.35, 50 degrees C, and mu = 1 M KCl) has been studied. In the presence of Zn(2+), the elimination reactions of both isomers occur from the Zn(2+)-complexed substrates (C). The equilibrium constants for the dissociation of the Zn(2+)-complexes are as follows: K(d) = 0.012 +/- 0.003 M (isomer 1) and K(d) = 0.065 +/- 0.020 M (isomer 2). The value of k(C)(H2O) for isomer 1 is 4.81 x 10(-6) s(-1). For isomer 2 both the rate constants for the "water" and OH(-)-induced reaction of the Zn(2+)-complexed substrate could be measured, despite the low concentration of OH(-) in the investigated reaction mixture [k(C)H2O)= 1.97 x 10(-6) s(-1) and k(C)(OH-)= 21.9 M(-1) s(-1), respectively]. The measured metal activating factor (MetAF), i.e., the reactivity ratio between the complexed and the uncomplexed substrate, is 8.1 x 10(4) for the OH(-)-induced elimination of 2. This high MetAF can be compared with the corresponding proton activating factor (Alunni, S.; Conti, A.; Palmizio Errico, R. J. Chem. Soc., Perkin Trans. 2 2000, 453), PAF = 1.5 x 10(6) and is in agreement with an E1cb irreversible mechanism (A(xh)D(E)* + D(N)) (Guthrie, R. D.; Jencks, W. P. Acc. Chem. Res. 1989, 22, 343). A value of k(C)(H2O)>or= 23 x 10(-7) s(-1) is estimated for the Cd(2+)-complexed isomer 2, while catalysis by Cd(2+) has not been observed for isomer 1.     

New organic nitrates. II. Synthesis of 2H-pyrido[2,3-e]-1,3-oxazine-2,4(3H)-diones, 2H-pyrido[4,3-e]-1,3-oxazine-2,4(3H)-diones, 2H-pyrido[4,3-e]-1,3-oxazin-4(3H)-ones, 2H-thieno[2,3-e]-1,3-oxazin-4(3H)-ones and 2H-thieno[3,4-e]-1,3-oxazin-2,4(3H)-diones

The preparation and the physico-chemical characterization of 2H-pyrido[2,3-e]-1,3-oxazine-2,4(3H)-diones, 2H-pyrido[4,3-e]-1,3-oxazine-2,4(3H)-diones, 2H-pyrido[4,3-e]-1,3-oxazin-4(3H)-ones, 2H-thieno[2,3-e]-1,3-oxazin-4(3H)-ones and 2H-thieno[3,4-e]-1,3-oxazine-2,4(3H)-diones are reported.     

Nature of plant stimulators in the production ofAcetobacter xylinum (“tea fungus”) biofilm used in skin therapy

Caffeine and related xanthines were identified as potent stimulators for the bacterial cellulose production in A. xylinum. These compounds are present in several plants whose infusions are useful as culture-medium supplements for this acetobacterium.

The proposed target for these native purine-like inhibitory substances is the novel diguanyl nucleotide phosphodiesterase(s) that participate(s) in the bacterial cellulogenic complex.

A better understanding of this feature of A. xylinum physiology may facilitate the preparation of bacterial cellulose pellicles, which are applied as a biotechnological tool in the treatment of skin burns and other dermal injuries.

     

New taxane derivatives: synthesis of baccatin[14,1-d]furan-2-one nucleus and its condensation with the norstatine side chain

New taxanes 15 and 18, containing the unsaturated and saturated baccatin[14,1-d]furan-2-one nucleus, respectively, were prepared starting from the readily available 13-oxo-7-Tes-baccatin III (3). Sequential formation of the enolate of 3 and reaction with ethyl glyoxylate gave the 13-oxo-7-Tes-baccatin[14,1-d]-3,4-dehydrofuran-2-one 4. The reduction of 4 can result in the formation of a mixture of compounds corresponding to 13-hydroxy alcohol 5 and 13-enol derivative 6. Both 5 and 6 were transformed into 13-oxo-7-Tes-baccatin[14,1-d]furan-2-one 8 by treatment with a base. Further reduction of 8 gave 13-hydroxy compound 9. Esterification of 6 and 9 with N,O-protected norstatine 12, followed by deprotection, gave the new promising anticancer taxanes 15 and 18, respectively.     

Selective synthesis of 14β-amino taxanes

The base induced deprotonation of H-14 of 7-triethylsilyl- (7-TES-) and 7-tert-butoxycarbonyl- (7-BOC-) protected 13-oxo-baccatins gave the corresponding enolates, which were selectively aminated with electrophilic nitrogen donors, such as azodicarboxylates and tosyl azide. In particular, tosyl azide gave the corresponding 7-BOC- and 7-TES-13-oxo-14β-azido-baccatin III. Alternatively, the last compound was prepared via NaN₃ induced azidation of the 13-silyl enol ether of 7-TES-13-oxo-baccatin III under oxidative (cerium ammonium nitrate) conditions. The 13-silyl enol ether was obtained in a multistep process by DBU induced silylation of 7-TES-13-oxo-baccatin III. The 7-TES-13-oxo-14β-azido-baccatin III was used as a key intermediate for the synthesis of a new family of antitumour taxanes containing amino based functional groups at the C-14 position, such as: 14β-azido, 14β-amino, 14β-amino 1, 14-carbamate, 14β-amino 1, 14-thiocarbamate, and 14β-amino N-tert-butoxycarbonyl-1,14-carbamate.     

Stereoselective Synthesis of Selenium-Containing Glycoconjugates via the Mitsunobu Reaction

A simple and efficient route for the synthesis of new glycoconjugates has been developed. The approach acts as a model for a mini-library of compounds with a deoxy-selenosugar core joined to a polyphenolic moiety with well-known antioxidant properties. An unexpected stereocontrol detected in the Mitsunobu key reaction led to the most attractive product showing a natural d-configuration. Thus, we were able to obtain the target molecules from the commercially available d-ribose via a shorter and convenient sequence of reactions.