Conformation of Tax-response elements in the human T-cell leukemia virus type I promoter

Background: HTLV I Tax is believed to activate viral gene expression by binding bZIP proteins (such as CRIB) and increasing their affinities for proviral THE target sites. Each 21 by THE target site contains an imperfect copy of the intrinsically bent CRE target site (the TRE core) surrounded by highly conserved flanking sequences. These flanking sequences are essential for maximal increases in DNA affinity and transactivation, but they are not, apparently, contacted by protein. Here we employ non-denaturing gel electrophoresis to evaluate TRE conformation in the presence and absence of bZIP proteins, and to explore the role of DNA conformation in viral transactivation.Results: Our results show that the TRE-1 flanking sequences modulate the structure and modestly increase the affinity of a CREB bZIP peptide for the TRE-1 core recognition sequence. These flanking sequences are also essential for a maximal increase in stability of the CREB-DNA complex in the presence of Tax.Conclusions: The CRE-like TRE core and the TRE flanking sequences are both essential for formation of stable CRIB-TRE-1 and Tax-CREB-TRE-1 complexes. These two DNA segments may have co-evolved into a unique structure capable of recognizing Tax and a bZIP protein.     

Platinum(IV)-mediated nitrile-sulfimide coupling: a route to heterodiazadienes

Pt(IV)-mediated addition of the sulfimide Ph2S = NH and the mixed sulfide/sulfimides o- and p-[PhS(=NH)](PhS)-C6H4 by the S=NH group to the metal-bound nitriles in the platinum(IV) complexes [PtCl4(RCN)2] proceeds smoothly at room temperature in CH2Cl2 and results in the formation of the heterodiazadiene compounds [PtCl4[NH=C(R)N=SR'Ph]2] (R' = Ph, R = Me, Et, CH2Ph, Ph; R' = o- and p-(PhS)C6H4; R = Et). While trans-[PtCl4(RCN)2] (R = Et, CH2Ph, Ph) reacting with Ph2S=NH leads exclusively to trans-[PtCl4[NH=C(R)N=SPh2]2], cis/trans-[PtCl4(MeCN)2] leads to cis/trans mixtures of [PtCl4[NH=C(Me)N=SPh2]2] and the latter have been separated by column chromatography. Theoretical calculations at both HF/HF and MP2//HF levels for the cis and trans isomers of [PtCl4[NH=C(Me)N=SMe2]2] indicate a higher stability for the latter. Compounds trans-[PtCl4[E-NH=C(R)N=SPh2]2] (R = Me, Et) and cis-[PtCl4[E-NH=C(Me)N=SPh2][Z-NH=C(Me)N=SPh2]] have been characterized by X-ray crystallography. The complexes [PtCl4[NH=C(R)N=SPh2]2] undergo hydrolysis when treated with HCl in nondried CH2Cl2 to achieve the amidines [PtCl4[NH=C(NH2)R]2] the compound with R = Et has been structurally characterized) and Ph2SO. The heterodiazadiene ligands, formed upon Pt(IV)-mediated RCN/sulfimide coupling, can be liberated from their platinum(IV) complexes [PtCl4[NH=C(R)N=SR'Ph]2] by reaction with Ph2PCH2CH2PPh2 (dppe) giving free NH=C(R)=SR'Ph and the dppe oxides, which constitutes a novel route for such rare types of heterodiazadienes whose number has also been extended. The hybrid sulfide/sulfimide species o- and p-[PhS(=NH)](PhS)C6H4 also react with the Pt(II) nitrile complex [PtCl2(MeCN)2] but the coupling--in contrast to the Pt(IV) species--gives the chelates [PtCl2[M-I=C(Me)N=S(Ph)C6H4SPh]]. The X-ray crystal structure of [PtCl2[M-I=C(Me)N=S(Ph)C6H4SPh-o]] reveals the bond parameters within the metallacycle and shows an unusual close interaction of the sulfide sulfur atom with the platinum.     

Conformational behaviour and inclusion compound forming properties of 5,18-disubstituted derivatives of 5, 11, 12, 18-tetrahydrotribenzo[b,f,j][1,4]diazacyclododecine-6, 17-dione

An X-ray structure analysis shows that the 5, 18-dimethyl derivative ($\text{5}$) of the title compound ($\text{4}$) crystallises from xylene as a 1:1 inclusion compound in which the host molecules adopt propeller-like conformations ($\text{7}$ and $\text{7}$*) with almost perfect $\text{C}$₂ symmetry. Dynamic ¹H n.m.r. spectroscopy shows that the 5, 18-dibenzyl derivative ($\text{6}$) of ($\text{4}$) forms a 1:1 inclusion compound with ethanol in the solid state and undergoes ring inversion ($\text{7}$ ? $\text{7}$*) between enantiomeric propeller-like conformations in solution against a barrier of 21.1 kcal mol^?1     

Chiral separation of halogenated amino acids by ligand-exchange capillary electrophoresis

The chiral separation of halogenated amino acids by ligand-exchange CE is described. Halogenated amino acids attracted increasing interest in recent years because of their physiological activities. Different chiral selectors, as there are L-4-hydroxyproline, L-histidine, and N-alkyl derivatives of L-4-hydroxyproline in form of their copper(II) complexes, are compared for their chiral recognition ability for halogenated amino acids. The influence of various parameters, such as selector concentration, pH, organic modifier, and field strength, on the resolution was investigated. All halogenated amino acids investigated were baseline-separated under optimized conditions.     

Intra- and intermolecular complexation in C6 monoazacoronand substituted cyclodextrins

The preparation of 6(A)-deoxy-6(A)-(6-(2-(1,4,7,10-tetraoxa-13-azacyclopentadecan-13-yl)acetamido)hexylamino)-alpha-cyclodextrin, 3, 6(A)-deoxy-6(A)-(6-(2-(1,4,7,10,13-pentaoxa-16-azacyclooctadecan-16-yl)acetamido)hexylamino)-alpha-cyclodextrin, 4, and their beta-cyclodextrin analogues, 5 and 6, are described. (1)H (600 MHz) ROESY NMR spectra of the C(6) substituted beta-cyclodextrins, 5 and 6, are consistent with the intramolecular complexation of their azacyclopentadecanyl- and azacyclooctadecanyl(acetamido)hexylamino substituents in the beta-cyclodextrin annulus in D(2)O at pD = 8.5 whereas those of their alpha-cyclodextrin analogues, 3 and 4 are not complexed in the alpha-cyclodextrin annulus. This is attributed to the monoazacoronand components of the substituents being able to pass through the beta-cyclodextrin annulus whereas they are too large to pass through the alpha-cyclodextrin annulus. However, the substituents of 3 and 4 are intermolecularly complexed by beta-cyclodextrin to form pseudo [2]-rotaxanes. Metallocyclodextrins are formed by 5 through complexation by the monoazacoronand substituent component for which log (K/dm(3) mol(-1))= <2, 6.34 and 5.38 for Ca(2+), Zn(2+) and La(3+), respectively, in aqueous solution at 298.2 K and I= 0.10 mol dm(-3)(NEt(4)ClO(4)).     

Magnetic Circular Dichroism Study of Analogues of the DNA Binding Ligands Netropsin and Distamycin A

UV absorption and MCD data of a complete series of netropsin-like oligopeptides containing between one and five N-methyl-pyrrole residues are reported. The presence of three MCD bands in the region between 220 and 350 nm can be related to the resonance of the peptide groups with the methylpyrrole systems of the oligopeptides. The longest wavelength absorption bands of all netropsin-like compounds investigated are ascribed to two electronic transitions of the resonance methypyrrole-carboxamide units. - Complex formation with DNA affects these MCD bands and hence modifies the transitions. This is explained by hypercon-jugation in the chromophoric system as a result of specific hydrogen bonding of peptide groups with dA·dT pairs of double stranded DNA.     

Many-to-many location-routing with inter-hub transport and multi-commodity pickup-and-delivery

In this paper, we consider a variant of the many-to-many location-routing problem, where hub facilities have to be located and customers with either pickup or delivery demands have to be combined in vehicle routes. In addition, several commodities and inter-hub transport processes are taken into account. A practical application of the problem can be found in the timber-trade industry, where companies provide their services using hub-and-spoke networks. We present a mixed-integer linear model for the problem and use CPLEX 12.4 to solve small-scale instances. Furthermore, a multi-start procedure based on a fix-and-optimize scheme and a genetic algorithm are introduced that efficiently construct promising solutions for medium- and large-scale instances. A computational performance analysis shows that the presented methods are suitable for practical application.     

On the liquid-crystalline properties of methacrylic polymers containing 4′-(4-alkyloxyphenyl)azobenzene mesogens

In this article, we report on the synthesis and thermotropic behaviour of methacrylic polymers containing 4′-(4-alkyloxyphenyl)azobenzene mesogens attached to the backbone through n-alkyloxy spacers of 6 or 10 methylene groups. Polymerisations were carried out via free radicals using azobisisobutyronitrile (AIBN) as initiator. Chemical structures of polymers and their precursors were characterised by ¹H NMR spectroscopy. Thermogravimetric analysis showed that azopolymers are thermally stable up to temperatures around 300°C. The thermotropic liquid-crystalline (LC) behaviour was studied by differential scanning calorimetry (DSC), polarized optical microscopy (POM) and X-ray diffraction (XRD). Results indicate that all synthesised mesogens, monomers and polymers developed two or more orthogonal LC phases in wide temperature ranges. Mesogens and monomers developed nematic and smectic phases, whereas polymers exhibited only smectic phase. In polymers, the arrangement of mesogens depends on the relative length of the spacer and the terminal flexible chain; two distinct structural models were proposed based on chemical interactions and steric constrains. The trans–cis photoisomerisation of monomers and polymers in solution was also studied. High cis-isomer contents (>80%) were reached in relative short irradiation times despite the steric constrains imposed by the polymer backbone.