Structural studies were performed on synthetic oligonucleotides with sequences corresponding to the P4/P6 and J3/4, J6/7 regions of the self-splicing group I intron of the bacteriophage T4 nrdB pre-mRNA, which correspond to the proposed triple-helical domain in the Tetrahymena thermophila intron. A 23-mer RNA was synthesized as a mixed ribo-deoxyribo oligonucleotide, modeling an expected base-paired region of P4 along with the J3/4 and P6 (5'-end bases of P6) regions. strand modeling the 3'-end bases of P6 and J6/7 regions, with which a triple helix may form, was synthesized as a pure oligoribonucleotide (7-mer RNA). The interactions of these oligonucleotides have been characterized by UV and circular dichroism (CD) spectroscopy. The results show that the 23-mer RNA forms a stable hairpin modeling the P4 base-paired region. Triple helix association between the 23-mer RNA hairpin and the 7-mer RNA single strand was detected by CD in the presence of Mg2+ (>5mM) but not in presence of a monovalent cation like Na+ (up to 500 mM). Studies on selected variants of both 7-mer and 23-mer RNAs were carried out. The results show that for the association of the two partner strands not only the formation of P6 helix but also triplet interactions between two strands are required. The association of the two strands in general follow a pattern predicted by comparative sequence analysis. Parallel studies on pure oligoribonucleotides having base sequence corresponding to those of the oligoribonucleotides showed no evidence of association under similar conditions, which could indicate that the 2'-hydroxyl groups of the riboses might play an important role in hydrogen bonding to form the required nucleoside triples. Molecular modeling studies on the proposed "plaited triple helix" formed by the association of the 23-mer RNA hairpin and 7-mer RNA single strand showed that the structure is sterically and energetically feasible.

A kinetic study on the pivaloyl chloride promoted H-phosphonate condensation step in the presence of differently substituted pyridines has been carried out. The kinetics of the system follow second order kinetics with a 1 : 1 ratio of nucleoside 3Ј-H-phosphonate and nucleoside component (with free 5-OH). Irrespective of the pyridine derivative used, the reaction rate is dependent on the concentration of this as well as of the hydroxy component and H-phosphonate. A reactive intermediate is indirectly identified from the kinetic evidence. This intermediate is suggested to be a pyridinium adduct formed by attack of the pyridine derivative on the initially formed mixed phosphonic carboxylic anhydride. Considerably lower rates of condensation in the presence of sterically hindered pyridines further support the existence of nucleophilic catalysis in the reactions with non-hindered pyridines. In addition, the rate of reaction in the presence of pyridines with pK a values above ∼4.8 is enhanced by an increase in pivaloyl chloride concentration. The main reason for this enhancement is most likely the fact that pivaloyl chloride removes pivalate ion, which retards the reaction by influencing the equilibrium between the mixed anhydride and the pyridinium intermediate. Although the observed rate constants are composed of several constants, their temperature dependence gives some indication of the nature of the transition-state of the rate-limiting step. Entropies of activation are estimated to be slightly positive, suggesting a transition state arising from attack of the hydroxy component on the pyridinium intermediate but involving a fair degree of bond breakage to the leaving group, i.e. the pyridine.

Several economical methods for geometry optimization, that should be applicable to larger molecules, have been evaluated for 19 phosphorus acid derivatives. MP2/cc-pVDZ geometry optimizations are used as reference points and the geometries obtained from the other methods are evaluated with respect to deviations in bond lengths and angles, from the reference geometries. The geometry optimization methods are also compared only about 0.5 and 0.55 kcal mol −1 respectively from the energies obtained with the reference geometries. Thus, use of HF/MIDI! for geometry optimization of phosphorus acids is a method that gives geometries of near-MP2 quality, resulting in a fair accuracy of energies in subsequent single point calculations, at a much lower computational cost other methods that give similar accuracies.

A large-scale armed conflict between Hezbollah and Israel in July 2006 caused the evacuation of a large number of Swedish residents from Lebanon. This report describes the evacuation throughout its various stages. Swedish authorities were prepared for an event of this type from the experience of the 2004 Asian tsunami disaster. Lessons learned from the management and medical care during the evacuations are presented in this report.

No abstract