Highly efficient photochemical 2'-deoxyribonolactone formation at the diagonal loop of a 5-iodouracil-containing antiparallel G-quartet

To explore the structure-dependent hydrogen abstraction in antiparallel and parallel G-quartet DNA structures, the photochemical reactivity of 5-iodouracil ((I)U)-containing human telomeric DNA 22-mers was investigated under the 302 nm UV irradiation conditions. We discovered that only antiparallel ODN 4, in which the second T residue in the diagonal loop of the antiparallel G-quartet is substituted with (I)U, was rapidly consumed as compared with parallel ODN 4 and the other (I)U-containing 22-mers under the irradiation conditions. Product analysis of the photolyzate of antiparallel ODN 4 indicated that a 2'-deoxyribonolactone residue was effectively produced at the 5' side of the (I)U residue in the diagonal loop. Photochemical 2'-deoxyribonolactone formation was also found in the (I)U-containing diagonal loop of antiparallel G-quartets d(GGGGTTT(I)UGGGG)(2) and d(GGGGTT(I)UTGGGG)(2), whereas the reaction did not occur at other DNA structures, including the single-stranded form, the loop region of the hairpin, and linear four-stranded G-quartets. The results clearly indicate that this type of 2'-deoxyribonolactone formation efficiently occurrs only in the diagonal loop of the antiparallel G-quartet. Furthermore, we found that 2'-deoxyribonolactone was formed at the (I)U-containing G-rich sequence of the IgG switch regions and the 5' termini of the Rb gene, suggesting the formation of an antiparallel G-quartet with a diagonal loop in these sequences. These results suggest that the present photochemical method can be used as a specific probe for the antiparallel G-quartet with the diagonal loop.     

Acceleration waves analyzed by a new continuum model of solids incorporating microscopic thermal vibrations

Acceleration waves propagating in isotropic solids at finite temperatures are studied by applying the method of singular surfaces to a new continuum model derived statistical-mechanically from a three-dimensional lattice model. The continuum model explicitly takes into account the microscopic thermal vibrations of the constituent atoms as one of the field variables. The propagation speeds and the ratios of mechanical and thermal amplitudes for both longitudinal and transverse waves are consistently determined. The differential equations that govern the time variation of the amplitudes of the waves are also derived. The analytical results, which are valid over a wide temperature range that includes the melting point, are evaluated numerically for several materials, and their physical implications are discussed. One of the findings to be emphasized is that of the singularities of the characteristic quantities at the melting point.Received: 13 March 2003, Accepted: 20 June 2003PACS: 62.30. + d, 65.40.-bM. Sugiyama: Correspondence to Dedicated to Prof. Ingo Müller on the occasion of his 65th birthday.     

Photochromic radical compounds based on a naphthopyran system

[reaction: see text] Naphthopyran derivatives with aminoxyl substituents (4a,b) gave the corresponding open-formed isomers (5a,b) by irradiation, which could be changed back to the starting closed-formed naphthopyrans by the treatment with SiO(2) as a catalyst. The tuning of intermolecular magnetic interactions between the isomer couples was found to be possible in these reversible systems.     

Derived Picard Groups of Finite-Dimensional Hereditary Algebras

Let A be a finite-dimensional algebra over a field k. The derived Picard group DPic _k (A) is the group of triangle auto-equivalences of D> ^b( mod A) induced by two-sided tilting complexes. We study the group DPic _k (A) when A is hereditary and k is algebraically closed. We obtain general results on the structure of DPic _k , as well as explicit calculations for many cases, including all finite and tame representation types. Our method is to construct a representation of DPic _k (A) on a certain infinite quiver ^irr. This representation is faithful when the quiver of A is a tree, and then DPic _k (A) is discrete. Otherwise a connected linear algebraic group can occur as a factor of DPic _k (A). When A is hereditary, DPic _k (A) coincides with the full group of k-linear triangle auto-equivalences of D^b( mod A). Hence, we can calculate the group of such auto-equivalences for any triangulated category D equivalent to D^b( mod A. These include the derived categories of piecewise hereditary algebras, and of certain noncommutative spaces introduced by Kontsevich and Rosenberg.     

Numerical analysis of turbulent flow separation in a rectangular duct with a sharp 180‐degree turn by algebraic Reynolds stress model

Turbulent flow in a rectangular duct with a sharp 180‐degree turn is difficult to predict numerically because the flow behavior is influenced by several types of forces, including centrifugal force, pressure‐driven force, and shear stress generated by anisotropic turbulence. In particular, this type of flow is characterized by a large‐scale separated flow, and it is difficult to predict the reattachment point of a separated flow. Numerical analysis has been performed for a turbulent flow in a rectangular duct with a sharp 180‐degree turn using the algebraic Reynolds stress model. A boundary‐fitted coordinate system is introduced as a method for coordinate transformation to set the boundary conditions next to complicated shapes. The calculated results are compared with the experimental data, as measured by a laser‐Doppler anemometer, in order to examine the validity of the proposed numerical method and turbulent model. In addition, the possibility of improving the wall function method in the separated flow region is examined by replacing the log‐law velocity profile for a smooth wall with that for a rough wall. The analysis results indicated that the proposed algebraic Reynolds stress model can be used to reasonably predict the turbulent flow in a rectangular duct with a sharp 180‐degree turn. In particular, the calculated reattachment point of a separated flow, which is difficult to predict in a turbulent flow, agrees well with the experimental results. In addition, the calculation results suggest that the wall function method using the log‐law velocity profile for a rough wall over a separated flow region has some potential for improving the prediction accuracy. Copyright © 2007 John Wiley & Sons, Ltd.     

Study of buried Si(1 1 1)-5 × 2-Au by surface X-ray diffraction

The structure of buried Si(1 1 1)-5 × 2-Au capped with amorphous Si was investigated using surface X-ray diffraction. It was found that the 5 × 2 structural periodicity is kept under the amorphous Si from the in-plane measurement. Furthermore, the intensity variation along the fractional-order rod indicates that Au atoms are located almost on the same plane.     

Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column.

We have developed an on-line automated system for phosphoproteome analysis using titania-based phosphopeptide enrichment followed by nanoLC-MS/MS. Titania beads were prepared by calcination of commercial chromatographic titania beads at 800 degrees C to convert the crystalline structure. The obtained rutile-form titania exhibited higher selectivity in phosphopeptide enrichment than commercial titania, even in the absence of a competitive chelating reagent for non-phosphopeptides. For phosphoproteome analysis of human cervical cancer HeLa cells, tryptic digests of the cell extracts were directly injected into this on-line system, and 696 non-redundant phosphopeptides with 671 unambiguously determined phosphorylation sites, derived from 512 phosphoproteins, were successfully identified. This is the first successful application of an on-line automated phosphoproteome analysis system to complex biological samples.