Computer modeling studies on the binding of 2',5'-linked dinucleoside phosphates to ribonuclease T1-influence of subsite interactions on the substrate specificity

The modes of binding of Gp(2',5')A, Gp(2',5')C, Gp(2',5')G and Gp(2',5')U to RNase T1 have been determined by computer modelling studies. All these dinucleoside phosphates assume extended conformations in the active site leading to better interactions with the enzyme. The 5'-terminal guanine of all these ligands is placed in the primary base binding site of the enzyme in an orientation similar to that of 2'-GMP in the RNase T1-2'-GMP complex. The 2'-terminal purines are placed close to the hydrophobic pocket formed by the residues Gly71, Ser72, Pro73 and Gly74 which occur in a loop region. However, the orientation of the 2'-terminal pyrimidines is different from that of 2'-terminal purines. This perhaps explains the higher binding affinity of the 2',5'-linked guanine dinucleoside phosphates with 2'-terminal purines than those with 2'-terminal pyrimidines. A comparison of the binding of the guanine dinucleoside phosphates with 2',5'- and 3',5'-linkages suggests significant differences in the ribose pucker and hydrogen bonding interactions between the catalytic residues and the bound nucleoside phosphate implying that 2',5'-linked dinucleoside phosphates may not be the ideal ligands to probe the role of the catalytic amino acid residues. A change in the amino acid sequence in the surface loop region formed by the residues Gly71 to Gly74 drastically affects the conformation of the base binding subsite, and this may account for the inactivity of the enzyme with altered sequence i.e., with Pro, Gly and Ser at positions 71 to 73 respectively. These results thus suggest that in addition to recognition and catalytic sites, interactions at the loop regions which constitute the subsite for base binding are also crucial in determining the substrate specificity.

Electronic excitations and alternation of conjugated polymers

The electronic excitations and fluorescence of conjugated polymers are related to large or small alternation ? of the transfer integrals t(1 ± ?) along the backbone. The fluorescence of polysilanes (PSs) and poly (para-phenylenevinylene (PPV) is linked to large ?, which places the one-photon gap Eg below the lowest two-photon gap Ea and reduces distortions due to electron-phonon (e-p) coupling. In contrast to small ? not, vert, similar 0.1 in ?-conjugated polymers, such as polyacetylene (PA), para-conjugated phenyls lead to an extended ?-system with increased alternation, to states localized on each ring and to charge-transfer excitations between them. Surprisingly good agreement is found between semiempirical parametric method 3 (PM3) bond lengths and exact Pariser-Parr-Pople (PPP) ?-bond orders for trans-stilbene, where the PPV bipolarons are confined to two phenyls. Stilbene spectra are consistent with increased alternation and small e-p distortions.

Excitation energy transfer in covalently linked pheophorbied—porphyrin systems

Steady-state fluorescence, lifetime measurements and time-resolved absorption spectra of the covalently linked hetero dimers consisting of pheophorbide and porphyrin revealed rapid (1011–1012s−1) and efficient singlet—singlet excitation energy transfer from porphyrin unit to pheophorbide.

Isolation and characterization of DNA polymerase epsilon from the silk glands of Bombyx mori

The silk gland of Bombyx mori, an endomitotically replicative tissue shows high levels of DNA polymerases alpha, delta, and epsilon activities. The ratio of polymerase alpha to that of delta plus epsilon is maintained at 1.1 to 1.3 in both the posterior and middle silk glands for the entire duration of late larval development. The three activities copurify in the initial stages of fractionation through phosphocellulose and DE52 but polymerase alpha gets resolved from the others on hydroxylapatite column. Separation between polymerase delta and epsilon is achieved by chromatography on QAE-Sephadex. DNA polymerase epsilon is a heterodimer comprising of 215- and 42-kDa subunits. The activity is maximum at pH 6.5 and the Km values for dNTPs vary between 3-9 microM. The enzyme possesses an intrinsically associated exonuclease activity which functions in the mismatch repair during DNA synthesis. Both polymerase and 3'-->5' exonuclease activities are associated with the 215-kDa subunit. By itself, DNA polymerase epsilon is processive and the catalytic activity is not enhanced by externally added bPCNA (Bombyx-proliferating cell nuclear antigen, an auxiliary protein for DNA polymerase delta). The enzyme resembles polymerase delta in having the exonuclease activity and in its response to aphidicolin or substrate analogs, but could be distinguished from the latter by its lack of response to the bPCNA and sensitivity to dimethyl sulfoxide. The two enzymes show partial immunological cross-reactivity with each other but no immunological relatedness to polymerase alpha. The absence of the repair enzyme DNA polymerase beta and the presence of substantial levels of polymerase epsilon in the silk glands suggest a possible role for the latter in DNA repair in that tissue.

New flame-retardant poly(pyromellitic imide aryl phosphoramide-ester)s

Flame-retardant poly(pyromellitic imide aryl phosphoramide-ester)s were synthesized by interfacial polycondensation of N,N?-bis(p-hydroxyphenyl)pyromellitic diimide with aryl phosphoramidic dichlorides. The polymers were characterized by IR and 1H-NMR spectroscopy. The molecular composition was confirmed by elemental analysis. The thermal stability and flammability of the polymers were studied by thermogravimetry and limiting oxygen index, respectively. Durch Grenzflächen-Polykondensation von N,N?-bis(4-hydroxyphenyl)pyromellitsäurediimid mit Dichloriden verschiedener Phosphoramide wurden flammhemmende Polymere erhalten. Diese wurden mittels IR- und 1H-NMR-Spektroskopie und Elementaranalyse charakterisiert. Thermische Stabilität und Entflammbarkeit wurden thermogravimetrisch bzw. durch Bestimmung des Sauerstoff-Indexes untersucht.

Novel photocrosslinkable liquid-crystalline polymers: poly[bis(benzylidene)] esters

A new class of photo-cross-linkable main-chain liquid crystalline polymers (PMCLCPs) containing bis(benzylidene)cycloallranone groups have been synthesized and studied for their liquid crystalline and photochemical properties. The bis(benzylidene)cycloalkanone group in the chain functions both as a mesogen and as a photoreactive center. All of the polymers exhibit a nematic mesophase. Two kinds of photoreactions, namely, photoisomerization and photo-cross-linking, operate in these polymers. Above Tu at the initial stages of irradiation, photoisomerization predominates the cross-linking, which resulta in the disruption of the chromophore aggregates. Below T8, because of the restricted mobility of the chains, only cross-linking takes place. Studies on the model compound, bis(benzylidene)cyclopentanone, confii the above observations and demonstrate further that the cross-linking proceeds by the 2r + 2r cycloaddition reaction of the bis(benzylidene)cycloallranone moieties. The cross-linking rate decreases with increase in the size of the cycloalkanone ring. Heating the solution cast polymer fii results in the ordered aggregation of the chromophores just above TI and also at the crystal to crystal transition temperature, which facilitates the phobcross-linking reactions. In the isotropic phase, the random orientation of the chromophores drastically curtails the cross-linking rata

Novel polymeric flame retardant plasticizers for poly(vinyl chloride)

Polyphosphate esters have been used as polymeric flame retardant plasticizers in poly(vinyl chloride); thermal and flammability studies were carried out to evaluate their efficiencies as fire retardants. A comparison is also made on the fire retardancy of the conventional simple phosphates with that of the polyphosphates as novel fire retardant plasticizers for PVC.

Reactivity of pyridinium poly(hydrogen fluoride) towards silicon tetrachloride, trichlorosilane and tris(amino)silanes

The reaction of silicon tetrachloride (SiCl4), trichlorosilane (HSiCl3) and tris(amino)silanes[(R2N)3SiH] with pyridinium poly(hydrogen fluoride) (PPHF) gives rise to hexafluorosilicatesalts in good yields. They have been characterized as pyridinium hexafluorosilicate(C5H5NH)2SiF6 (in the case of SiCl4 and HSiCl3) and the corresponding dialkyl ammoniumhexafluorosilicate (R2NH2)2SiF6 salts [for tris(amino)silanes] (where R2N=pyrrolidino,piperidino, hexamethyleneimino, morpholino, N-methylpiperazino and diethylamino). Theinteresting features of these reactions are the cleavage of Si---Cl, Si---H and Si---N bondsat room temperature by PPHF and fluorination of the silicon moiety to a hexa-coordinateddoubly charged anionic species. These compounds have been characterized by NMR (1H,29Si, 19F) and IR spectroscopy, and by chemical analysis.

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Electron-beam irradiation effects on poly(ethylene-co-vinyl acetate) polymer

Poly(ethylene-co-vinyl acetate) (EVA) films were irradiated with a 1.2MeV electron beam at varied doses over the range 0-270kGy in order to investigate the modifications induced in its optical, electrical and thermal properties. It was observed that optical band gap and activation energy of EVA films decreased upon electron irradiation, whereas the transition dipole moment, oscillator strength and number of carbon atoms per cluster were found to increase upon irradiation. Further, the dielectric constant, the dielectric loss, and the ac conductivity of EVA films were found to increase with an increase in the dose of electron radiation. The result further showed that the thermal stability of EVA film samples increased upon electron irradiation.

Poly-ols Based Sol-Gel Synthesis of Zinc Oxide Thin Films

We demonstrate that the structural and optical properties of a sol-gel deposited zinc oxide thin film can be tuned by varying the composition of the sol, consisting of ethylene glycol and glycerol. A systematic study of the effect of the composition of sol on the mean grain size, thickness, and defect density of the zinc oxide film is presented. About 20% glycerol content in the sol is observed to improve the quality of the film, as evaluated by X-ray diffraction and photoluminescence studies. Thus, optimizing the composition of the sol for about 60 nm thick ZnO film using 20% glycerol resulted in the zinc oxide film that is about 80% transparent in visible spectrum, exhibiting electrical resistivity of about 18 Omega cm and field-effect mobility of 0.78 cm(2)/(V s). (C) 2010 The Electrochemical Society. DOI: 10.1149/1.3515894] All rights reserved.

The Design and Construction of Synthetic Protein Mimics

A strategy for the modular construction of synthetic protein mimics based on the ability non-protein amino acids to act as stereochemical directors of polypeptide chain folding, is described. The use of alpha-aminoisobutyric acid (Aib) to construct stereochemically rigid helices has been exemplified by crystallographic and spectroscopic studies of several apolar peptides, ranging in length from seven to sixteen residues. The problem of linker design in elaborating alpha,alpha motifs has been considered. Analysis of protein crystal structure data provides a guide to choosing linking sequences. Attempts at constructing linked helical motifs using linking Gly-Pro segments have been described. The use of flexible linkers, like epsilon-aminocaproic acid has been examined and the crystallographic and solution state analysis of a linked helix motif has been presented. The use of bulky sidechain modifications on a helical scaffold, as a means of generating putative binding sites has been exemplified by a crystal structure of a peptide packed in a parallel zipper arrangement.

Second harmonic generation in poled molecularly doped polymer films : Push-pull butadienes in poly(methyl methacrylate) and polystyrene

We report second harmonic generation in a new class of organic materials, namely donor-acceptor substituted all-trans butadienes doped in poly(methyl methacrylate) or polystyrene and oriented by corona poling at elevated temperatures. Second harmonic measurements were made at room temperature. The observed d33 coefficients are greater than those of potassium dihydrogen phosphate or 4-dimethylamino-4'-nitrostilbene doped in similar polymer matrices. Rotational diffusion coefficients estimated from the decay characteristics of the second harmonic intensity in the polymer films indicate that the polymer matrix plays a major role in stabilizing the dopants in a nonlinear optics conducive environment.

Synthesis and studies of Rh(I) catalysts within and across poly(alkyl aryl ether) dendrimers

In order to study the efficiencies of catalytic moieties within and across dendrimer generations, partially and fully functionalized dendrimers were synthesized. Poly(alkyl aryl ether) dendrimers from zero to three generations, presenting 3 to 24 peripheral functionalities, were utilized to prepare as many as 12 catalysts. The dendrimer peripheries were partially and fully functionalized with triphenylphosphine in the first instance. A rhodium(I) metal complexation was performed subsequently to afford multivalent dendritic catalysts, both within and across generations. Upon synthesis, the dendritic catalysts were tested in the hydrogenation of styrene, in a substrate-to-catalyst ratio of 1:0.001. Turn-over-numbers were evaluated for each catalyst, from which significant increases in the catalytic activities were identified for multivalent catalysts than monovalent catalysts, both within and across generations. (C) 2010 Elsevier B.V. All rights reserved.

Dendritic Poly(ether imine) Based Gene Delivery Vector

The nonviral vector based gene delivery approach is attractive due to advantages associated with molecular-level modifications suitable for optimization of vector properties. In a new class of nonviral gene delivery systems, we herein report the potential of poly(ether Mine) (PETIM) dendrimers to mediate an effective gene delivery function. PETIM dendrimer, constituted with tertiary amine branch points, n-propyl ether linkers and primary amines at their peripheries, exhibits significantly reduced toxicities, over a broad concentration range. The dendrimer complexes pDNA effectively, protects DNA from endosomal damages, and delivers to the cell nucleus. Gene transfection studies, utilizing a reporter plasmid pEGFP-C1 and upon complexation with dendrimer, showed a robust expression of the encoded protein. The study shows that PETIM dendrimers are hitherto unknown novel gene delivery vectors, combining features of poly(ethylene imine)-based polymers and dendrimers, yet are relatively nontoxic and structurally precise.