Design and structural analysis of hairpin-TFO for transcriptional activation of genes in S-cerevisiae

Triplex forming oligonucleotides (TFOs) have the potential to modulate gene expression. While most of the experiments are directed towards triplex mediated inhibition of gene expression the strategy potentially could be used for gene specific activation. In an attempt to design a strategy for gene specific activation in vivo applicable to a large number of genes we have designed a TFO based activator-target system which may be utilized in Saccharomyces cerevisiae or any other system where Gal4 protein is ectopically expressed. The total genome sequence of Saccharomyces cerevisiae and expression profiles were used to select the target genes with upstream poly (pu/py) sequences. We have utilized the paradigm of Gal4 protein and its binding site. We describe here the selection of target genes and design of hairpin-TFO including the targeting sequences containing polypurine stretch found in the upstream promoter regions of weakly expressed genes. We demonstrate, the formation of hairpin-TFO, its binding to Gal4 protein, its ability to form triplex with the target duplex in vitro, the effect of polyethylenimine on complex formation and discuss the implication on in vivo transcription activation.

An improved X-ray structural analysis for determining cation distribution in ZnFe2O4 and ZnFe2O4- Fe3O4 solid solutions

The distribution of zinc cation between crystallographically nonequivalent positions in ZnFe204 has been determined by anomalous X-ray scattering near the Zn K absorption edge. Measured intensity ratio with two energies close to the edge can be quantitatively explained only by assigning all zinc cations to the tetrahedral position in the approximately cubic close packed array of oxygen ions. A similar conclusion has also been reached for ZnxFe3-x04 solid solutions with x = 0.73, 0.54 and 0.35 employing the improved X-ray method. This is consistent with the EXAFS results which indicate an almost unchanged environmental structure around zinc cation in these solid solutions.

Synthesis, structural analysis and solvatochromic behaviour of 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile mesogen

In this communication, we report the synthesis and characterisation of a new luminescent liquid crystalline material, 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile (3). We have confirmed its structure by Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy, elemental analysis and X-ray single crystal diffraction studies. The newly synthesised compound crystallises in a monoclinic system with the space group C2/c and its cell parameters are found to be a?=?25.181(4) angstrom, b?=?15.651(4)angstrom, c?=?12.703(19) angstrom, V?=?4880.4 (16) angstrom, Z?=?8. The results indicate that the presence of weak CH center dot center dot center dot O and CH center dot center dot center dot N hydrogen bonding as short-range intermolecular interactions are responsible for the formation of its crystal assembly. The measured torsion angle shows the existence of a distorted structure for the molecule wherein 4-butoxyphenylene ring substituent at the fourth position of the central pyridine ring forms a torsion angle chiC(4), C(3), C(10), C(19)] of 40.55 degrees. Its liquid crystalline behaviour was investigated with the aid of polarised optical microscopy and differential scanning calorimetry. The study reveals that the compound displays a broad nematic phase in the range of 78112 degrees C. Further, solution phase optical studies indicate that it is a blue light emitter in different non-polar and polar organic solvents at a concentration of 10-5M.

Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities

Antifolates are competitive inhibitors of dihydrofolate reductase ( DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the `supersite' and classified supersites of DHFRs from 56 species into 16 `site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondar

Structural analysis of plate-type fuel assemblies and development of a non-destructive method to assess their integrity

This work is concerned with the structural behaviour and the integrity of parallel plate-type nuclear fuel assemblies. A plate-type assembly consists of several thin plates mounted in a box-like structure and is subjected to a coolant flow that can result in a considerable drag force. A finite element model of an assembly is presented to study the sensitivity of the natural frequencies to the stiffness of the plates' junctions. It is shown that the shift in the natural frequencies of the torsional modes can be used to check the global integrity of the fuel assembly while the local natural frequencies of the inner plates can be used to estimate the maximum drag force they can resist. Finally a non-destructive method is developed to assess the resistance of the inner plates to bear an applied load. Extensive computational and experimental results are presented to prove the applicability of the method presented. © 2013 Elsevier B.V. All rights reserved.

Structural analysis of nickel doped cobalt ferrite nanoparticles prepared by coprecipitation route

Magnetic nanoparticles of nickel substituted cobalt ferrite (NixCo1-xFe2O4:0 <= x <= 1) have been synthesized by co-precipitation route. Particles size as estimated by the full width half maximum (FWHM) of the strongest X-ray diffraction (XRD) peak and transmission electron microscopy (TEM) techniques was found in the range 18-28 +/- 4 nm. Energy dispersive X-ray (EDX) analysis confirms the presence of Co, Ni, Fe and oxygen as well as the desired phases in the prepared nanoparticles. The selective area electron diffraction (SAED) analysis confirms the crystalline nature of the prepared nanoparticles. Data collected from the magnetization hysteresis loops of the samples show that the prepared nanoparticles are highly magnetic at room temperature. Both coercivity and saturation magnetization of the samples were found to decrease linearly with increasing Ni-concentration in cobalt ferrite. Superparamagnetic blocking temperature as determined from the zero field cooled (ZFC) magnetization curve shows a decreasing trend with increasing Ni-concentration in cobalt ferrite nanoparticles. (C) 2009 Elsevier B.V. All rights reserved.

Structural analysis of monoterpene glycosides extracted from Paeonia lactiflora Pall. using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and high-performance liquid chromatography/electrospray ionization tandem mass spectrometry

Paeoniflorin standard was first investigated by electrospray ionization Fourier transform ion cyclotron resonance tandem mass spectrometry (ESI-FTICR-MS/MS) using a sustained off-resonance irradiation (SORI) collision-induced dissociation (CID) method at high mass resolution. The experimental results demonstrated that the unambiguous elemental composition of product ions can be obtained at high mass resolution. Comparing MS/MS spectra and the experimental methods of hydrogen and deuterium exchange, the logical fragmentation pathways of paeoniflorin have been proposed. Then, the extracts of the traditional Chinese medicine Paeonia lactiflora Pall. were analyzed by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). By comparison with the ESI-FTICR-MS/MS data of paeoniflorin, the isomers paeoniflorin and albiflorin in Paeonia lactiflora Pall. have been identified using HPLC/MS with CID in an ion trap and in-source CID. Furthermore, using the characteristic fragmentation pathways, the retention times (t(R)) in HPLC and MS/MS spectra, the structures of three other kinds of monoterpene glycoside compounds have been identified on-line without time-consuming isolation.

Structural analysis of selected characteristic flavones by electrospray tandem mass spectrometry

Seven structure analogical flavonoid aglycones have been analyzed using electrospray ionization tandem mass spectrometry (ESI-MSn) in the negative-ion mode. The spectra obtained ESI-MSn allowed us to propose plausible schemes for their fragmentation mechanism. By analyzing the product ions spectra of deprotonated molecule ions [M-H](-), some neutral diagnostic losses and specific retro Diels-Alder fragments were obtained. By using all of these characteristic fragment ions we can specially differentiate the flavone isomer.