Characterization of species-specific repeated DNA sequences from B. nigra

The construction and characterization of two genome-specific recombinant DNA clones from B. nigra are described. Southern analysis showed that the two clones belong to a dispersed repeat family. They differ from each other in their length, distribution and sequence, though the average GC content is nearly the same (45%). These B genome-specific repeats have been used to analyse the phylogenetic relationships between cultivated and wild species of the family Brassicaceae.

Developmental regulation of cytochrome P-450 (b+e) and glutathione transferase (Ya+Yc) gene expression in rat liver

The expression of cytochrome P-450 (b+e) and glutathione transferase (Ya+Yc) genes has been studied as a function of development in rat liver. The levels of cytochrome P-450 (b+e) mRNAs and their transcription rates are too low for detection in the 19-day old fetal liver before or after phenobarbitone treatment. However, glutathione transferase (Ya+Yc) mRNAs can be detected in the fetal liver as well as their induction after phenobarbitone treatment can be demonstrated. These mRNAs contents as well as their inducibility with phenobarbitone are lower in maternal liver than that of adult nonpregnant female rat liver. Steroid hormone administration to immature rats blocks substantially the phenobarbitone mediated induction of the two mRNA families as well as their transcription. It is suggested that steroid hormones constitute one of the factors responsible for the repression of the cytochrome P-450 (b+e) and glutathione transferase (Ya+Yc) genes in fetal liver.

Molecular Modeling Studies on Amphotericin B and its Complex with Phospholipid,

Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-to-tail dimeric structure and lipid - amphotericin B complex demonstrate interesting features of the flexibilities within the molecule and define the optimal interactions for the formation of a stable dimeric structure and complex with phospholipid.

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

CD and NMR studies on the aggregation of amphotericin-B in solution

We report in this paper the aggregation properties of amphotericin-B (amp-B) in solution using CD and 1H-NMR techniques. Our results indicate that the preferred structure of amp-B in dimethylsulfoxide is a monomer at low concentrations (10−4M and below) and a stable dimer at higher concentrations (range 5 · 103 M to 10−2M). In a DMSO/ethanol mixture (1:1 (v/v)), the antibiotic is monomeric, irrespective of the concentration within the range studied. We propose a head-to-tail model based on NMR data. An understanding of the head-to-tail dimer, is, we believe important, particularly in view of the recent report wherein it is proposed that the drug inserts into bilayers as head-to-tail oligomers.

Coupled substitution of niobium and silicon in potassium titanyl phosphate and arsenate (KTiOPO4 and KTiOAsO4. Synthesis and nonlinear optical properties of KTi1-xNbxOX1-xSixO4 (X = P, As)

Coupled substitution of Nb(V) and Si(IV) for Ti(IV) and P(V)/As(V) in KTiOP04 (KTP) and KTiOAsO4 (KTA) giving new series of nonlinear optical materials, KTi1-xNbxOX1-xSixO4 (X=P,As), has been investigated. Substitution up to x = 0.40 readily occurs, the members retaining the orthorhombic (Pna2(1)) structure of KTP. The second harmonic generation (SHG) property of the parent KTP and KTA is not adversely affected by the coupled substitution. SHG intensity of the powder samples of the X = P series shows a slight increase with x up to x = 0.15; for 0.15 < x less-than-or-equal-to 0.40, there is a decrease in SHG intensity as compared to that for KTP. A similar trend in SHG intensity is seen for the arsenic analogs.

Kaon B parameter with Wilson fermions

We calculate the kaon B parameter in quenched lattice QCD at beta=6.0 using Wilson fermions at kappa=0.154 and 0.155. We use two kinds of nonlocal (''smeared'') sources for quark propagators to calculate the matrix elements between states of definite momentum. The use of smeared sources yields results with much smaller errors than obtained in previous calculations with Wilson fermions. By combining results for p=(0,0,0) and p=(0,0,1), we show that one can carry out the noperturbative subtraction necessary to remove the dominant lattice artifacts induced by the chiral-symmetry-breaking term in the Wilson action. Our final results are in good agreement with those obtained using staggered fermions. We also present results for B parameters of the DELTAI = 3/2 part of the electromagnetic penguin operators, and preliminary results for B(K) in the presence of two flavors of dynamical quarks.

Molecular structure of Lantadene-B&C, triterpenoids ofantana camara, red variety: Lantadene-B, 22β-angeloyloxy-3-oxoolean-12-en-28-oic acid; Lantadene-C, 22 β-(S)-2′-methyl butanoyloxy-3-oxoolean-12-en-28-oic acid

(I)Lantadene-B: C35H52O5,M r =552.80, MonoclinicC2,a=25.65(1),b=6.819(9),c=18.75(1) Å,beta=100.61(9),V=3223(5) Å3,Z=4,D x =1.14 g cm–3 CuKagr (lambda=1.5418A),mgr=5.5 cm–1,F(000)=1208,R=0.118,wR=0.132 for 1527 observed reflections withF o ge2sgr(F o ). (II)Lantadene-C: C35H54O5·CH3OH,Mr=586.85, Monoclinic,P21,a=9.822(3),b=10.909(3),c=16.120(8)Å,beta=99.82(4),V=1702(1)Å3,Z=2,D x =1.145 g cm–3, MoKagr (lambda=0.7107Å), mgr=0.708 cm–1 F(000)=644,R=0.098, wR=0.094 for 1073 observed reflections. The rings A, B, C, D, and E aretrans, trans, trans, cis fused and are in chair, chair, sofa, half-chair, chair conformations, respectively, in both the structures. In the unit cell the molecules are stabilized by O-HctdotO hydrogen bonds in both the structures, however an additional C-HctdotO interaction is observed in the case of Lantadene-C.

On The Temperature-Dependence of Regioselectivity in the Amination of Bromobenzotropones

The ipso/cine ratio in the amination of 5-bromo-2,3-benzo- or 2-bromo-4,5-benzotropone shows a dependence upon the temperature at which the reaction is conducted, changing in favour of the ipso-product when the temperature is maintained high, ruling out an aryne-type mechanism. A comparison of independent mechanisms envisaged for the formation of the two isomeric products suggests a two-part reason: (i) at a higher reaction temperature, C-protonation, a step necessary for the formation of the cine-product, could be retarded when a direct internal mode is interfered with by a less efficient external one, and (ii) reketonisation by elimination of bromide, needed to form the ipso-product, is likely to have a high temperature coefficient enabling the rate of its formation to overtake that of the cine-product.

Palladium(II) chloride complexes of bis(pyrazolyl)cyclotriphosphazenes

Reactions of the bis(3,5-dimethylpyrazolyl)cyclotriphosphazene derivatives gem-N3P3(MeNCH(2)CH(2)O)(2)(dmp)(2) (1) and nongeminal cis-N3P3(OPh)(4)(dmp)(2) (2) with PdCl2 afford complexes of the type [PdCl2.(L)] (L = 1 or 2). In these complexes, the phosphazenes act as bidentate NN-donor ligands with the two pyrazolyl pyridinic nitrogen atoms bonded to the metal, thus forming a six- and an eight-membered chelate ring, respectively. The structures of 2 and [PdCl2.(2)] (4) have been confirmed by single-crystal X-ray diffraction. Crystal data for 2: a = 16.759(2) Angstrom, b = 10.788(3) Angstrom, c = 19.635(9) Angstrom, beta = 101.61(3)degrees, P2(1/c), Z = 4, R = 0.038 for 4688 reflections with F > 5 sigma(F). Crystal data for 4: a = 9.701(3) Angstrom, b = 24.853(4) Angstrom, c = 15.794(4) Angstrom, beta = 101.46(2)degrees, P2(1/n), Z = 4, R = 0.030 for 5416 reflections with F > 5 sigma(F).

Reactions of copper(I) aryloxides with phenyl isothiocyanate: steric and ligand control in the oligomerization of [N-phenylimino(aryloxy)methanethiolato]copper(I) complexes

The preparation of five different copper(I) complexes [CuSC(=NPh)(OAr)}L(n)]m (1-5) formed by the insertion of PhNCS into the Cu-OAr bond and the crystal structure analyses of three of them have been carried out. A monomeric species 1 (OAr = 2,6-dimethylphenoxide) is formed in the presence of excess PPh3 (n = 2, m = 1) and crystallizes as triclinic crystals with a = 12.419(4) angstrom, b = 13.298(7) angstrom, c = 15.936(3) angstrom, alpha = 67.09(3)-degrees, beta = 81.63(2)-degrees, gamma = 66.54(3)-degrees, V = 2224(2) angstrom3, and Z = 2. The structure was refined by the least-squares method to final R and R(w) values of 0.038 and 0.044, respectively, for 7186 unique reflections. Copper(I) 2,5-di-tert-butyl-4-methylphenoxide results in the formation of a dimeric species 2 in the presence of P(OMe)3 (n = 1, m = 2), where the coordination around Cu is trigonal. Crystals of 2 were found to be orthorhombic with a = 15.691(2) angstrom, b = 18.216(3) angstrom, c = 39.198(5) angstrom, v = 11204(3) angstrom3, and Z = 8. Least-squares refinement gave final residuals of R = 0.05 and R(w) = 0.057 with 6866 unique reflections. A tetrameric species 3 results when PPh3 is replaced by P(OMe)3 in the coordination sphere of copper(I) 2,6-dimethylphenoxide. It crystallizes in the space group P1BAR with a = 11.681 (1) angstrom, b = 13.373(2) angstrom, c = 20.127(1) angstrom, a = 88.55(l)-degrees, beta = 89.65(l)-degrees, gamma = 69.28(1)-degrees, V = 2940(l) angstrom3, and Z = 2. Least-squares refinement of the structure gave final values of 0.043 and 0.05 for R and R(w) respectively using 12214 unique reflections. In addition, a dimeric species 4 is formed when 1 equiv of PPh3 is added to the copper(I) 4-methylphenoxide, while with an excess of PPh3 a monomeric species 5 is isolated. Some interconversions among these complexes are also reported.

Stereochemical properties and x-ray structure of a water-soluble diastereomeric (arene)ruthenium(II) Schiff-base complex: [Ru(.eta.-MeC6H4Pri-p)(H2O)(L*)](ClO4), containing a weakly bound aqua ligand [HL* = (S)-(.alpha.-methylbenzyl)salicylaldimine]

An air-stable and water-soluble diastereomeric half-sandwich ruthenium(I1) complex, [Ru(s-MeCsH4Pr'-p)(H*O)-(L*)] (C104) (l), has been isolated and structurally characterized [HL* = (27)-(a methylbenzyl)salicylaldimine,2-HOC6H4CH-NCHMePhI. Complex 1, Czd-I3oNO&lRu, crystallizes in the noncentric triclinic space group P1 with a = 9.885(1) A, b = 10.185(1) A, c = 14.187(2) A, a = 110.32(1)', 6 = 102.17(1)', y = 102.41(1)O, V=1243( 1) A3, and 2 = 2. The X-ray structure shows the presence of two diastereomers in a 1:l ratio having RR,,,SCand SR,,,&c onfigurations. The Ru-OHz bond distances are considerably long, and the values for RR, - a~n d SRu-1isomers are 2.1 19(5) and 2.203(5) A, respectively. The aqua complex (1) exists as a single diastereomer in solution,and it forms stable adducts with P-, N-, and halide-donor ligands. The stereochemical changes associated with adduct-forming reactions follow an inversion order: PPhs >> P(OMe)3 > pyridine bases >> halides (I, Br, Cl) >H20.

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

Syntheses, spectroscopy, structures, and conformations of .lambda.3-cyclotriphosphazanes: role of negative hyperconjugation

The reactions of As-chlorocyclotriphosphazane [EtNPCl], with phenols or trifluoroethanol yield the respective aryloxy- or trifluoroethoxy-containingX 3-cyclotriphosphazanes [EtNP(OR)]3 (R = C6H4Br-4 (2),C 6H5 (3C,6 H3-Mez-3,5 (4), C6H3Mez-2,6 (5), CH2CF3 (6)) as their cis-transisomericmixtures. The products have beencharacterized by IRand NMRspectroscopy. Thecrystalstructuresofboth thecis (2a) and trans(2b) isomer_softhep-bromophenoxy derivative have been determined by X-ray diffraction. Crystal data for 2a: triclinic, P1, a = 9.872(4) A, b = 13.438(6) A, c = 13.548(8) A, CY = 117.02(5)', 0 = 96.00(6)', y = 105.38(4)O, Z = 2, final R = 0.080. Crystal data for 2b: monoclinic, P21/n, a = 12.721(6) A, b = 13.468(7) A, c = 17.882(5) A, /3 = 101.62(3)O, Z = 4, final R = 0.066. The cis isomer exhibits a chair-triaxial conformation and the trans isomer a boat-triaxial conformation. Conformational preferences of X3-cyclotriphosphazanes have been probed by both MNDO and ab initio calculations on model systems [HNPXIp (X = H, F). In addition to vicinal lone pair repulsions, negative hyperconjugative interactions involving the nitrogen lone pairs and adjacent P-X Q* orbitals are found to be important (especially when X is an electronegative substituent) in determining the conformational preferences of X3-cyclotriphosphazanes. The calculations also show that the axial - equatorial conversion at phosphorus has a large activation barrier in these systems

Synthesis of Isoquinolines from Indanones-Total Synthesis of Illudinine

Schmidt reaction of 5-methoxy or 7-methoxyindan-1-ones or their derivatives results exclusively in isocarbostyrils which are converted into 6-methoxy or 8-methoxyisoquinolines in good yields. This strategy has been extended to the total synthesis of illudinine methyl ester (1b) starting from methyl 8-methoxy-2,2-dimethyl-7-oxo-1,2,3,5,6,7-hexahydro-s-indacene-4-carboxylate (4).