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.

     

Oxysulfide Sm(2)Ti(2)S(2)O(5) as a stable photocatalyst for water oxidation and reduction under visible light irradiation (lambda < or = 650 nm)

A Ti-based oxysulfide, Sm(2)Ti(2)S(2)O(5), was studied as a visible light-driven photocatalyst. Under visible light (440 nm < or = lambda < or = 650 nm) irradiation, Sm(2)Ti(2)S(2)O(5) with a band gap of approximately 2 eV evolved H(2) or O(2) from aqueous solutions containing a sacrificial electron donor (Na(2)S-Na(2)SO(3) or methanol) or acceptor (Ag(+)) without any noticeable degradation. This oxysulfide is, therefore, a stable photocatalyst with strong reduction and oxidation abilities under visible-light irradiation. The electronic band structure of Sm(2)Ti(2)S(2)O(5) was calculated using the plane-wave-based density functional theory (DFT) program. It was elucidated that the S3p orbitals constitute the upper part of the valence band and these orbitals make an essential contribution to the small band gap energy. The conduction and valence bands' positions of Sm(2)Ti(2)S(2)O(5) were also determined by electrochemical measurements. It indicated that conduction and valence bands were found to have satisfactory potentials for the reduction of H(+) to H(2) and the oxidation of H(2)O to O(2) at pH = 8. This is consistent with the results of the photocatalytic reactions.     

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.

     

A new method for characterizing solid surface acidity - an infrared spectroscopic method using probe molecules such as N2 and rare gases

A new infrared-spectroscopic method to characterize acid sites of zeolites using small and weakly basic molecules such as diatomic and monoatomic molecules is reviewed. It has been revealed that N2 is an effective probe molecule to characterize both Brønsted acidity and Lewis acidity of H-form zeolites. The characteristics of the N 2 probe are discussed in detail in comparison with the CO probe. O2 and rare gases have also been applied to monitor the strong acid sites in the H-form zeolites. Further, the studies of the adsorption of water on H-form zeolites are shortly reviewed: a recent IR study of the H₂ ¹⁸O adsorption on H-ZSM-5 has given direct experimental evidence that the main feature of the observed IR bands is due to the hydrogen-bonded adsorption of water on the Brønsted acid sites.     

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.