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.

     

Helicity‐Encoded Molecular Strands: Efficient Access by the Hydrazone Route and Structural Features

Control over the folding of molecular strands may be achieved by appropriate choice of the constituting subunits, in particular for chains of specific heterocycles such as sequences of directly connected pyridine (py) and pyrimidine (pym) rings, which are known to fold into extended helical structures. Since the hydrazone (hyz) group represents an isomorphic analogue of a py site, the condensation of hydrazine and carboxaldehyde derivatives of pym offers a very efficient approach to strands incorporating hyz instead of py units and constituted by sequences of alternating hyz and pym groups. A series of such strands of different lengths, up to ten hyz units, i.e., 1 – 7 , were synthesized. Their spectral properties indicate that they fold indeed into helical shapes. Extensive characterization was performed in solution by ¹HNMR spectroscopy and in the solid state by determination of the crystal structures of eight such strands. They all display the expected helical geometry with up to 3 ¹/₃ turns and direct stacking contacts. The efficiency and flexibility of the synthetic approach as well as its wide potential for generation of diversity through lateral decoration make the (hyz? pym) subunit a particularly attractive helicity codon.     

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

Solvolysen von 4-Alkylidenbicyclo[3.2.0]hept-2-en-6-olen. Synthese von 1-Vinylfulvenen und 8,8-Diphenylheptafulven

Solvolysis of 4-Alkydenbicyclo[3.2.0]hept-2-en-6-oles. Synthesis of 1-Vinylfulvenes and 8,8-Diphenylheptafulvene Four 4-alkylidenebicyclo[3.2.0]hept-2-en-6-ones 2–5 , obtained via ketene cycloaddition to fulvenes, were reduced to separated mixtures of the ‘endo’ -alcohols ‘endo’- 6 to ‘endo’- 9 (68–73%) and ‘exo’- 6 to ‘exo’- 9 (3–20%). Treatment of some of these alcohols with (CF₃SO₂)₂O in CH₂Cl₂/pyridine caused a spontaneous solvolysis to yield unsaturated 7-membered rings as pyridinium triflates 10–12 or 1-vinylfulvenes 13 and 14 , a new class of reactive tetraenes: Both ‘endo’- 9 and ‘exo’- 9 , having two methyl groups at C(7), were converted into the vinylfulvene 13 (≈ 80%). The alcohols with two H-atoms at C(7) exhibited a stereochemically controlled reaction selectivity, inasmuch as ‘endo’- 6 to ‘endo’- 8 afforded only the corresponding 7-membered-ring pyridinium salts 10–12 (66–79%), while ‘exo’- 6 produced only the vinylfulvene 14 (77%). A stereoelectronic control argument explains the C(1), C(5)-bond cleavage with ‘endo’- B and ‘endo’– 6 -‘endo’- 8 , as well as the C(1), C(7)-bond cleavage with ‘exo’- B , ‘exo’- 6 , and with both ‘endo’- and ‘exo’- 9 . Thermolysis (120°) of the pyridinium triflates 10 and 11 yielded the 3-isopropenyl-cycloheptatrienes 18 and 19 , respectively (≈90%); similar conditions (145°) applied to the triflate 12 produced the doubly cyclized fluorene derivative 21 (60%). When the iodide 22 derived from the triflate 12 with Nal was heated in refluxing toluene, 8,8-diphenylheptafulvene ( 23 , 86%) was obtained.     

Determination of chlormequat and mepiquat in pear,tomato, and wheat flour using on-line solid-phase extraction (Prospekt) coupled with liquid chromatography-electrospray ionization tandem mass spectrometry

A new methodology based on pressurized liquid extraction (PLE) followed by LC-MS is presented for the simultaneous and unequivocal determination of alkylphenol ethoxylates (APEOs) and their degradation products, alkylphenols (APs) and alkylphenoxy carboxylates (APECs), in sediment samples. The protocol, applicable to a full range of APEO oligomers and degradation products, permits the sensitive and selective determination of APEOs (nEO = 1-15), APECs (nEO = 0-1) and APs at low ppb levels (LODs = 1-5 microg/kg) in sediment samples. Optimization of the operational parameters of PLE clearly demonstrates that significant thermal losses of APs occur during extraction at elevated temperatures. The loss of octylphenol (OP) at 100 degrees C was 61.2% and of nonylphenol (NP) 40.0%, whereas other compounds were completely recovered. Thus, to avoid losses due to the volatility of alkylphenols, a low extraction temperature should be applied. The conditions that gave the best results for all target compounds were as follows: extraction solvent mixture, methanol-acetone (1:1, v/v); temperature, 50 degrees C; pressure, 1500 p.s.i.; two static cycles. Using PLE and a subsequent clean-up with solid-phase extraction (SPE), the simultaneous extraction of APEOs, APs and APECs from sediment samples was achieved yielding recoveries >70% and producing low MS background noise. The developed methodology was applied on a routine basis to the analysis of alkylphenolic compounds in sediment samples. APEOs and their persistent degradation products were detected in significant concentrations in sediments from Portuguese rivers, especially at sites situated in the proximity of industrial plants (mainly the textile industry). The total concentration of alkylphenolic compounds (APEOs+APs+APECs) ranged from 155 to 2400 microg/kg. Of all the alkylphenolic compounds, NP comprised 40 to 50% with concentrations up to 1172 microg/kg.     

Synthese,Kristallstruktur und festkörper‐NMR‐spektroskopische Untersuchung neuer Oxonitridosilicate der Mischkristallreihe Ba4−xCaxSi6N10O

The new oxonitridosilicates Ba_4?xCa_xSi₆N₁₀O have been synthesized by means of high‐temperature synthesis in a radio‐frequency furnace, starting from calcium, barium, silicon diimide and amorphous silicon dioxide. The maximum reaction temperature was at about 1450 °C. The solid solution series Ba_4?xCa_xSi₆N₁₀O with a phase width 1.81 ≤ x ≤ 2.95 was obtained. The crystal structure of Ba_1.8Ca_2.2Si₆N₁₀O was determined by X‐ray single‐crystal structure determination (P2₁3, no. 198), a = 1040.2(1) pm, Z = 4, wR2 = 0.082). It can be described as a highly condensed network of corner‐sharing SiN₄ and SiON₃ tetrahedra, the voids of which are occupied by the alkaline earth ions. The structure is isotypic with that of BaEu(Ba_0.5Eu_0.5)YbSi₆N₁₁. In the ²⁹Si solid‐state MAS‐NMR spectrum two isotropic resonances at ?50.0 and ?53.6 ppm were observed.