Uridine binding by Zn(II) macrocyclic complexes: diversion of RNA cleavage catalysts

Zn(II) complexes of 1-oxa-4,7,10-triazacyclododecane (12[ane]N3O), 1,5,9-triazacyclododecane (12[ane]N3), and 1-hydroxyethyl-1,4,7-triazacyclononane (9[ane]N3OH) promote cleavage of the RNA analogue, 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) at pH 8.0, I=0.10 M (NaCl), 25 degrees C with second-order rate constants of 8.9x10(-3), 9.0x10(-3), and 3.3x10(-3) M-1 s-1, respectively. Cleavage of HpPNP by these catalysts is inhibited by uridine with inhibition constants (Ki) of 1.2, 0.46, and 45 mM, respectively, under these conditions. Binding constants derived from these inhibition constants are 2-200-fold larger than those for binding of related Zn(II) complexes to phosphate diesters under similar conditions, suggesting that uridine sequences in RNA will inhibit Zn(II)-catalyzed cleavage by competing with phosphate diester binding sites. Further studies are carried out that utilize pH-potentiometric titrations to monitor uridine binding to five Zn(II) macrocyclic complexes in aqueous solution at 25 degrees C, I=0.10 M (NaCl). The data are consistent with binding of the Zn(II) complexes to the N3-deprotonated form of uridine to give log KU.-values of 5.29, 4.57, 4.56, 3.47, and 2.65 for the Zn(II) complexes of 12[ane]N3, 12[ane]N4, 12[ane]N3O, 15[ane]N3O2, and 9[ane]N3OH, respectively (12[ane]N4=1,4,7,10-tetraazacyclododecane, 15[ane]N3O2=1,4-dioxa-7,10,13-triazacyclopentadecane). For the five Zn(II) complexes studied, there is a linear relationship between uridine anion binding constants and hydroxide binding constants.     

Study of phase transition and volume thermal expansion in a rare-earth (RE) oxyfluoride system by high-temperature XRD (RE=La, Nd, Sm, Eu and Gd)

Volume thermal expansion behaviour of a number of rare-earth oxyfluorides (REOF) have been studied using high-temperature X-Ray diffractometry (HT-XRD) in the 298–1075 K range in air. The studies revealed an anomalous expansion for each compound associated with phase transition. The phase transition temperature and the coefficient of volume thermal expansion of five compounds in REOF series determined by this method are reported and compared with our earlier results obtained by dilatometry.     

Automated RNA tertiary structure prediction from secondary structure and low‐resolution restraints

A novel protocol for all‐atom RNA tertiary structure prediction is presented that uses restrained molecular mechanics and simulated annealing. The restraints are from secondary structure, covariation analysis, coaxial stacking predictions for helices in junctions, and, when available, cross‐linking data. Results are demonstrated on the Alu domain of the mammalian signal recognition particle RNA, the Saccharomyces cerevisiae phenylalanine tRNA, the hammerhead ribozyme, the hepatitis C virus internal ribosomal entry site, and the P4–P6 domain of the Tetrahymena thermophila group I intron. The predicted structure is selected from a pool of decoy structures with a score that maximizes radius of gyration and base–base contacts, which was empirically found to select higher quality decoys. This simple ab initio approach is sufficient to make good predictions of the structure of RNAs compared to current crystal structures using both root mean square deviation and the accuracy of base–base contacts. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Experimental and Theoretical Investigations of Structural Isomers of Dichalcogenoimidodiphosphinate Dimers: Dichalcogenides or Spirocyclic Contact Ion Pairs?

A synthetic protocol for the tert-butyl-substituted dichalcogenoimidodiphosphinates [Na(tmeda){(EPtBu(2))(2)N}] (3 a, E=S; 3 b, E=Se; 3 c, E=Te) has been developed. The one-electron oxidation of the sodium complexes [Na(tmeda){(EPR(2))(2)N}] with iodine produces a series of neutral dimers (EPR(2)NPR(2)E--)(2) (4 b, E=Se, R=iPr; 4 c, E=Te, R=iPr; 5 a, E=S, R=tBu; 5 b, E=Se, R=tBu; 5 c, E=Te, R=tBu). Attempts to prepare 4 a (E=S, R=iPr) in a similar manner produced a mixture including HN(SPiPr(2)). Compounds 4 b, 4 c and 5 a-c were characterised by multinuclear NMR spectra and by X-ray crystallography, which revealed two alternative structures for these dimeric molecules. The derivatives 4 b, 4 c, 5 a and 5 b exhibit acyclic structures with a central chalcogen-chalcogen linkage that is elongated by approximately 2 % (E=S), 6 % (E=Se) and 8 % (E=Te) compared to typical single-bond values. By contrast, 5 c adopts an unique spirocyclic contact ion-pair structure in which a [(TePtBu(2))(2)N](-) ion is Te,Te' chelated to an incipient [(TePtBu(2))(2)N](+) cyclic ion. DFT calculations of the relative energies of the two structural isomers indicate a trend towards increasing stability for the contact ion pair relative to the corresponding dichalcogenide on going from S to Se to Te for both the isopropyl and tert-butyl series. The two-electron oxidation of [Na(tmeda){(EPtBu(2))(2)N}] (E=S, Se, Te) with iodine produced the salts [(EPtBu(2))(2)N](+)X(-) (7 a, E=S, X=I(3); 7 b, E=Se, X=I; 7 c, E=Te, X=I), which were characterised by X-ray crystallography. Compound 7 a exists as a monomeric, ion-separated complex with [d(S--S)=2.084(2) A]; 7 b and 7 c are dimeric [d(Se--Se)=2.502(1) A; d(Te--Te)=2.884(1) A].     

In vitro biomolecular interaction studies and cytotoxic activities of copper(II) and zinc(II) complexes bearing ONS donor thiosemicarbazones

Among all the bio‐metals, zinc and copper derivatives of ONS donor thiosemicarbazone have aroused great interest because of their potential biological applications. Multisubstituted thiosemicarbazone ligand H₂dspt (3,5‐dichlorosalicylaldehyde‐N⁴‐phenylthiosemicarbazone) derived new ternary complexes like [Zn(dspt)(phen)]?DMF ( 1 ) and [Cu(dspt)(phen)]?DMF ( 2 ), and another thiosemicarbazone, H₂dsct (3,5‐dichlorosalicylaldehyde‐N⁴‐cyclohexylthiosemicarbazone), derived [Cu(dsct)(bipy)]?DMF ( 3 ). These complexes have been characterized by elemental analysis (CHNS), Fourier transform infrared (FT‐IR), ultraviolet–visible (UV–Vis) and proton nuclear magnetic resonance (¹H‐NMR) spectra. The structures of the complexes were obtained by single‐crystal X‐ray diffraction analysis. Compounds 1 and 2 got crystallized in the monoclinic P2₁/c space group. The complexes showed interesting supramolecular interaction, which in turn stabilizes the complexes. The ground state electronic configurations of the complexes were studied using the B3LYP/LANL2DZ basis set, and ESP plots of complexes were investigated. The interaction of the complexes with calf thymus DNA (CT‐DNA) was studied using absorption and fluorescence spectroscopic methods. A UV study of the interaction of the complexes with calf thymus DNA (CT‐DNA) has shown that the complexes can effectively bind to CT‐DNA, and [Cu(dspt)(phen)]·DMF ( 2 ) exhibited the highest binding constant to CT‐DNA (K_b = 3.7 × 10⁴). Fluorescence spectral studies also indicated that Complex 2 binds relatively stronger with CT DNA through intercalative mode, exhibiting higher binding constant (K_q = 4.7 × 10⁵). The DNA cleavage result showed that the complexes are capable of cleaving the DNA without the help of any external agent. Molecular docking studies were carried out to understand the binding of complexes with the molecular target DNA. Complex 2 exhibited the highest cytotoxicity against human breast cancer cell line MD‐MBA‐231 (IC₅₀ = 23.93 μg/mL) as compared to Complex 1 (IC₅₀ = 44.40 μg/mL) .     

Working group report: Quantum chromodynamics sub-group

This is the report of the QCD working sub-group at the Tenth Workshop on High Energy Physics Phenomenology (WHEPP-X).      

Low-energy behavior of the 3He(α, γ)7Be cross section

Cross sections for the ³He(α, γ)⁷Be reaction have been measured at several energies from E_c.m. = 165 to 1169 keV by counting prompt γ-rays from a windowless, differentially pumped, recirculating, ³He gas target. The cross-section factor S₃₄(E_c.m.) and branching ratio γ₁/γ₀ were determined at each energy. Cross sections were also measured at E_c.m. = 947 and 1255 keV by counting the γ-rays from the ⁷Be produced in a ³He gas cell with a Ni entrance foil. Combining the results of these two independent experiments yields a zero-energy intercept for the cross-section factor of S₃₄(0) = 0.53 ± 0.03 keV · b. The relationship between these measurements and several theoretical calculations, and the import of the extrapolated cross section for the solar-neutrino problem are discussed.     

Reduction of anxiety during MR imaging: a controlled trial

An anxiety reduction protocol was developed and evaluated for routine use with neurology and neuropsychiatry patients undergoing brain or spinal scans. Thirty five patients underwent standard procedures, with limited information given in advance. Twenty nine experimental patients received a booklet giving information about the scanning procedure and advice on cognitive strategies for anxiety reduction, a tape-recorded demonstration of scanner noise, a visit to the control room before entering the scanner, a device to signal for adjustment of music volume, precise timings of each scan, and a clock visible during scanning. Anxiety was measured before, during, and after scanning, using subjective ratings and a retrospective version of the Spielberger State Anxiety Scale. There was no difference in anxiety between groups immediately prior to the scan and immediately after entering the scanner. Patients in the experimental group were significantly less anxious during the scan than control patients, as measured by mean anxiety ratings made during the imaging procedure and by retrospective State Anxiety scores completed immediately after leaving the scanner. The results show that scan-related anxiety can be reduced by introducing these simple changes to MR imaging procedures, with minimal cost, no special training of staff, and no disruption of the running of the MR Unit.