RNA-catalyzed RNA ligation on an external RNA template

Variants of the hc ligase ribozyme, which catalyzes ligation of the 3' end of an RNA substrate to the 5' end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3'-hydroxyl to the 5'-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside 5'-triphosphates onto the 3' end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.     

Bending of DNA by asymmetric charge neutralization: all-atom energy simulations

DNA dodecamers of the alternating d(CG).d(CG) sequence with six phosphate groups either charge-neutralized or substituted by neutral methylphosphonates across the major or minor groove have been subjected to energy minimization to determine the conformational effect of the asymmetric elimination of phosphate charge. We report bending angles, directions of bending, and detailed structural characteristics such as groove widths and local base-pair parameters. Our principal results are that charge neutralization on one face of the DNA induces significant bending toward the neutralized face, in agreement with theoretical predictions on a simplified model and experimental data on a similar base-pair sequence, and that the DNA conformation averaged over all stereospecific methylphosphonate substitutions is nearly the same as the conformation produced by charge neutralization of the phosphates. Individual isomers, however, cover a wide range of structures, with the magnitude and direction of overall bending sensitive to the precise stereochemical pattern of neutralization. Our simulation does not explicitly contain counterions, and the results therefore suggest that counterions can influence DNA structure by neutralizing the phosphate charge. These data provide new hints into the molecular mechanisms which underlie the deformations of DNA structure induced by the binding of positively charged proteins and other tightly associated cationic species.     

Synthesis, crystal structure, spectroscopic and thermal properties of [Et4N][Ta6Br12(H2O)6]Br4·4H2O (Et=ethyl)—A new compound with the paramagnetic [Ta6Br12] cluster core

A new hexanuclear cluster compound, [Et₄N][Ta₆Br₁₂(H₂O)₆]Br₄·4H₂O (Et=ethyl) (1), with the paramagnetic [Ta₆Br₁₂]³⁺ cluster entity, was synthesized and characterized by elemental and TG/DTA analyses, IR and UV/Vis spectroscopy and by a single-crystal X-ray diffraction study. The presence of the paramagnetic [Ta₆Br₁₂]³⁺ unit was confirmed also by the room-temperature magnetic and EPR measurements. The compound crystallizes in the tetragonal I4₁/a space group, with a=14.299(5), c=21.241(5) Å, Z=4, R₁(F)/wR₂(F²)=0.0296/0.0811. The structure contains discrete [Ta₆Br₁₂(H₂O)₆]³⁺ cations with an octahedron of metal atoms edge-bridged by bromine atoms and with water molecules occupying all six terminal positions. The cluster units are positioned in the vertices of the three-dimensional (pseudo)diamond lattice. The structure shows similarities with literature reported structures of cluster compounds crystallizing in the diamond space group.     

Spatially resolved micro-X-ray fluorescence and micro-X-ray absorption fine structure study of a fractured granite bore core following a radiotracer experiment

Spatially resolved X-ray absorption and fluorescence investigation with a micrometer-scale resolution on actinide-containing samples provide information necessary for safety assessment of nuclear waste disposal. In this paper one example of such an experiment is presented. This example entails neptunium speciation in a fractured granite bore core from the Swedish Äspö Hard Rock Laboratory following a radiotracer experiment using µ-XAFS and µ-XRF. In order to probe micro-volumes below the surface in the granite samples and thereby avoid potential changes in the Np speciation during cutting of the bore core, a confocal irradiation–detection geometry is employed. µ-XAFS results for a selected granite bore core cross section with ~ 3 nmol Np/g reveal that Np, originally introduced as Np(V) in the tracer cocktail, is present in the granite in its reduced Np(IV) form. The Np(IV) is often present as particles, tens of µm in size. Elemental distribution maps show the tracer Np to be located in fissures and permeable channels not larger than 100 µm. The Np distribution appears often correlated with Zn also present in some fissures. We observe small granite fissures containing Fe (presumably Fe(II)), where we do not detect any Np. It is feasible that inflowing Np(V) has a shorter residence time in large fractures, while in the smaller fissures migration is slower, leading to longer residence times, i.e., reaction times, where it is reduced to less soluble Np(IV) and becomes thereby immobilized.     

Defect Structure in Te-doped GaAs Single Crystals after Plastic Deformation (II). Dislocation Slip and Cell Formation

At temperatures above the brittle-to-ductile transition (490 °C) in Te-doped GaAs three types of predominant defect configurations have been observed after uniaxial compression along a [001] direction: (i) twins and stacking faults (500 … 520 °C), (ii) slip zones of dislocations (≈550 °C) and (iii) dislocation cells (580 … 590 °C). In Part II quantitative details of the appearance of slip and cell formation are given. Leading segments of gliding half loops are mainly of 60° type. Cell walls were formed by multiple slip of perfect dislocations.     

Bis­(tetra­methyl­ammonium) hexa­molyb­date hydrate, [(CH3)4N]2[Mo6O19]·H2O

The crystal and molecular structure of the title compound, (C₄H₁₂N)₂[Mo₆O₁₉]·H₂O, has been determined from X‐ray diffraction data. The poly­oxo­anion [Mo₆O₁₉]^2? is built up from six distorted MoO₆ octa­hedra sharing common edges and one common vertex at the central O atom, and has crystallographic m3m (O_h) symmetry. The cation has crystallographic 3m symmetry.     

Synthese und Fluoreszenzeigenschaften von cyansubstituierten 2-Aminopyridinen

The synthesis of several 2-aminopyridines is described. The reaction of tetracyanoethylene with 3-imino-propane-carbonitrile gives 2-amino-3,4,5-tricyano-pyridines with alkyl and aryl-substituents, resp., in position 6. Nucleophilic substitution of 2-amino-6-chloro-3,5-dicyanopyridines and 2-amino-6-chloro-3,4,5-tricyano-pyridines with phenolates leads to a variety of pyridines. Spectroscopical data of absorption and fluorescence are presented and the influence of the cyano groups is discussed. The results are in good agreement with quantum chemical calculations (PPP).

Herrn Univ-Prof. Dr.A. Holasek zum 60. Geburtstag gewidmet.     

Zur Kenntnis der anomalen Reaktionen bei der Aminostickstoffbestimmung. III. Die Anomalie einiger Aminosäuren

Zusammenfassung In der vorliegenden Arbeit wurde versucht, einen Einblick in die bisher ungeklärte anomale Reaktion verschiedener Aminosäuren mit salpetriger Säure zu gewinnen. Es wird wahrscheinlich gemacht, daß bei der Desaminierung der Aminosäuren nicht nur eine Hydroxyverbindung entsteht, sondern auch die entsprechende Nitrolsäure. Bei den -Aminosäuren wird dabei Kohlendioxyd in Freiheit gesetzt. Das Ausmaß der Bildung von Nitrolsäure hängt von der Konzentration der Nitritlösung ab; unter den Bedingungen der Aminostickstoffbestimmung entstehen etwa 30%. Die Nitrolsäure ist der Ausgangspunkt für die anomale Gasentwicklung. Bei Temperaturerhöhung reagiert nämlich die Isonitrosogruppe der Nitrolsäure mit salpetriger Säure, wobei unter Entwicklung von N₂ und N₂O die entsprechende Carbonylverbindung entsteht. Bei Tyrosin bilden sich noch zusätzliche Gasmengen infolge der anomalen Reaktion der Phenolgruppierung. Bei Cystin rührt das Mehrvolumen von der Reaktion der Disulfidgruppierung mit salpetriger Säure her.

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Summary This study reports on an effort to gain an insight into the previously unexplained anomalous reaction of various amino acids with nitrous acid. It is made probable that not only is a hydroxyl compound formed during the deamination but also the corresponding nitrolic acid. In the case of -amino acids, carbon dioxide is also liberated. The extent of the formation of nitrolic acid depends on the concentration of the nitrite solution; under the conditions of the amino nitrogen determination about 30% is produced. The nitrolic acid is the starting point for the anomalous production of gas. When the temperature is increased, the isonitroso group of the nitrolic acid reacts with nitrous acid, and the corresponding carbonyl compound results along with evolution of N₂ and N₂O. In the case of tyrosine, additional amounts of gas arise because of the anomalous reaction of the phenol grouping. In the case of cystine, the excess volume comes from the reaction of the disulfide grouping with nitrous acid.

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Résumé Dans le présent travail les auteurs cherchent à éclaircir les réactions anormales de différents aminoacides sur l'acide nitreux. Ils ont établi selon toute vraisemblance que lors de la désamination des aminoacides il ne se forme pas seulement une combinaison hydroxylée mais également l'acide nitrolique correspondant. Lors de cette réaction les -amino-acides libèrent de l'anhydride carbonique. L'importance de la formation d'acide nitrolique dépend de la concentration de la solution nitreuse; dans les conditions de la détermination de l'azote aminé il s'en forme environ 30%. L'acide nitrolique constitue le point de départ des dégagements gazeux anormaux. Lors d'une élévation de température le groupement isonitrosé de l'acide nitrolique réagit notamment avec l'acide nitreux en donnant naissance à la combinaison carbonylée correspondante avec dégagement simultané de N₂ et N₂O. Avec la tyrosine il se forme en outre des quantités de gaz supplémentaires dues à la réaction anormale du groupement phénol. Avec la cystine c'est la réaction du groupement disulfure sur l'acide nitreux qui donne lieu à un dégagement gazeux supplémentaire.

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7. Mitteilung: Anomalie der Sulfonsäureamide 1.     

Trends in 19F-19F and 29Si-19F coupling constants in organosilicon derivatives containing SiF2 and Si2F4 units

Consideration of ¹⁹F-¹⁹F and ²⁹Si-¹⁹F coupling constants in a series of organosilicon derivatives containing SiF₂ and Si₂F₄ units reveals a number of trends which are useful for structural and stereochemical assignments. For example the vicinal ¹⁹F-¹⁹F coupling constants in a number of CSiF₂SiF₂C- derivatives (including straight chain compounds, disilacyclobutanes and disilacyclohexanes) show an apparent linear dependence on dihedral angle, varying in magnitude from near zero for small values of φ up to ca. 19 Hz for φ ～ 180°. This is particularly useful for stereochemical assignments [1,2]. In addition ²⁹Si-¹⁹F coupling constants appear to fall in quite distinct ranges (¹J_SiF > 300 Hz, 29 Hz < ²J_SiF < 55 Hz, ³J_SiF < 10 Hz). This is quite useful for structural assignments [1,6]. Reaction of SiF₂ with 1,3-cyclohexadiene gives two new silicon fluorine compounds: a disilabicyclo[2,2,2]octene and an HSi₂F₅-substituted cyclohexadiene.