Multiple binding modes of the camptothecin family to DNA oligomers

The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].     

Determination of Formation Regions of Titanium Phosphates; Determination of the Crystal Structure ofβ-Titanium Phosphate, Ti(PO4)(H2PO4), from Neutron Powder Data

The formation region of the various types of layered titanium hydrogen phosphate hydrates was investigated. The materials were prepared by hydrothermal methods, treating amorphous titanium phosphate with phosphoric acid (8 to 16M) in the temperature range 175 to 250°C. The materials obtained were:α-Ti(HPO₄)₂·H₂O,γ-Ti(PO₄)(H₂PO₄)·2H₂O, and its anhydrous formβ-Ti(PO₄)(H₂PO₄). The structure ofβ-Ti(PO₄)(H₂PO₄) has been determined by Rietveld powder refinement of high resolution neutron diffraction data. The structure is refined in the monoclinic space groupP2₁/n(No. 14). The unit cell parameters are:a=18.9503(4) Å,b=6.3127(1) Å,c=5.1391(1) Å,β=105.366(2)°;Z=4. The final agreement factors were:R_p=2.9% andR_wp=3.8%. The structure ofβ-Ti(PO₄)(H₂PO₄) is built from TiO₆octahedra linked together by tertiary phosphate (PO₄) and dihydrogen phosphate ((OH)₂PO₂) tetrahedra. The layers are held together by hydrogen bonds.     

Independence versus indetermination: basis of two canonical clustering criteria

Advances in Data Analysis and Classification - This paper aims at comparing two coupling approaches as basic layers for building clustering criteria, suited for modularizing and clustering very...     

Thioacetylacetone: structural and vibrational assignments.

Thioacetylacetone and its variously deuterated isotopomers have been investigated using electronic and vibrational spectroscopy combined with quantum chemical calculations. Thioacetylacetone is known for its photochromic properties, but the structures of the initial and final forms have been the subject of a long debate. Analysis of the IR spectra recorded in low-temperature argon and xenon matrices, room-temperature solutions, and in the gas phase has allowed us to establish the nature of the photochromic species and of its precursor. Similar to the case of another beta-thioxoketone, monothiodibenzoylmethane, the photo-product has been assigned to the nonchelated SH exo-rotamer of the (Z)-enethiol tautomeric form, whereas the dominant ground-state species corresponds to the chelated (Z)-enol tautomeric form. Detailed vibrational assignments have been proposed for both forms based on quantum chemical calculations and polarization experiments. In the case of the chelated (Z)-enol species prevailing in the ground state, a second-order perturbative anharmonic analysis at the B3LYP/cc-pVTZ level indicated strong anharmonic effects associated with the intramolecular hydrogen bond, leading to a shift of more than 600 cm-1 of the wavenumber of the OH-stretching vibration. A small fraction of the SH endo-rotameric chelated (Z)-enethiol form was also detected under unperturbed conditions. The (Z)-enethiol form can be converted into the (Z)-enol form by irradiation at 290 nm.     

Thermochemical excess properties of multicomponent systems: Representation and estimation from binary mixing data

A general equation for the estimation of thermodynamic excess properties of multicomponent systems from observed excess properties of the various binary combinations of the components has been developed, based on a simple model of the multicomponent system. This estimation takes the form $$\Delta \bar Z_{12...N}^{ex} = \sum\limits_{i = 1}^N {\sum\limits_{j > i}^N {(X_i + X_j )(f_i + f_j )(\Delta \bar Z_{ij}^{ex} )^* } } $$ in which \((\Delta \bar Z_{ij}^{ex} )^* \) is the molar excess property (enthalpy, entropy, volume, free energy, etc.), of the binary system with components at the same molar ratio as in the multicomponent system, and f_i, f_j are weighted mole fractions using weighting factors based on the excess properties of the binary systems. The important features of this equation are: it is applicable to a broad range of thermodynamic properties, its application to both integral and differential mixing properties is independent of the manner in which the binary mixing data is represented (Redlich-Kister equation, Wilson equation, etc.), and it provides reasonably accurate predictions ranging from quite good for simple systems of nonspecific interactions to only fair for associated solutions. This equation is recommended as a point-of-departure for mathematical representation of experimental data for multicomponent systems.     

Hydrogel networks of poly(ethylene oxide) star-molecules supported by expanded polytetrafluoroethylene membranes: characterization, biocompatibility evaluation and glucose diffusion characteristics

The present work discusses the grafting by electron beam irradiation of poly(ethylene oxide) (PEO) star-shaped polymers onto porous expanded polytetrafluoroethylene (EXPTFE) surfaces. The resulting materials are intended to combine the good biocompatible properties of PEO with the outstanding mechanical properties of PTFE. The star-shaped PEOs were synthesized via anionic polymerization. 3 Mev electron beam irradiation was applied to graft these PEO stars onto porous EXPTFE surfaces. The hydrophobic EXPTFE surface had to be pre-modified with N-vinylpyrrolidone. ESCA was used to quantify the amount of grafted star-shaped PEO. Unmodified EXPTFE surfaces are well known, when implanted in a body, to be rapidly covered by a layer of cells and fibrin. The EXPTFE coated with PEO were implanted in the peritoneal cavity of rats (or under the back skin). This implantation did not induce any inflammation reactions and SEM analysis had attested the absence of adsorbed cells and fibrin. The glucose diffusion properties of these membranes were studied by a lag time analysis method and compared to those of pure PEO hydrogels. As expected, glucose diffuses through the hydrogel coated membrane and diffusion is not affected by the presence of the EXPTFE membrane.     

Synthesis of 5,6-dihydro-4H-thiopyran-4-ones

The anions of 1,4-diaryl-3-buten-2-ones 1 reacts with arylisothiocyanates, yielding intermediates 4 which can ring close to 5,6-dihydro-4H-thiopyran-4-ones 5 . Under similar reaction conditions ethyl 3-oxo-4-pentenoates 7 gives the 6-spiropyrans 9 . Methylation of 3 gives the S-methylated open form 6 .     

Formation of the monoanion [Ar*P(BH3)(mu-BH2)2H]- with a symmetrically bridging hydride from the attempted synthesis of the dianion [Ar*P(BH3)3]2-

Addition of an excess of BunLi to the bis(borano)phosphide complex [Ar*PH(BH3)2]-Li+ 1 (Ar* = 2,4,6-tri-tert-butylphenyl) and subsequent treatment with BH3, gives the anionic complex [Ar*P(BH3)(mu-BH2)2H]-Li+ 2 instead of the expected tris(borano)phosphide dilithium, [Ar*P(BH3)3]2-2Li+ 3.     

Temperature-sensitive polypeptide brushes-coated mesoporous silica nanoparticles for dual-responsive drug release

A multifunctional nanohybrid based on mesoporous silica nanoparticle and biocompatible polypeptide was fabricated for targeted and dual-responsive therapy of tumor cells.     

End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.