Universal fluorescent labeling of amplification products using locked nucleic acids

Amplification/hybridization‐based genetic analyses using primers containing locked nucleic acids (LNAs) present many benefits. Here, we developed a novel design for universal fluorescent PCR using LNAs. Universal fluorescent PCR generates intermediate nonlabeled fragments and final fluorescent fragments in a two‐step amplification process that uses locus‐specific primers with universal tails and universal fluorescent primers. In this study, a few standard nucleotides were replaced with LNAs only in the fluorescent universal primers. The sequence of the fluorescent universal primer significantly affected the amplification efficiency. For primers with three LNAs, the fluorescent primers with stable M13(‐47) sequences provided the most efficient signal (approximately tenfold higher than the primers with M13(‐21) sequences at lower Tm values). Moreover, AT‐rich LNA substitutions in the fluorescent primers produced much lower amplification efficiencies than GC‐rich substitutions. GC‐rich LNAs produced greater differences in Tm values among primers, and resulted in the preferential production of fluorescently labeled amplicons. The specificity and sensitivity of LNA‐containing fluorescent primers were assessed by genotyping eight STRs in Japanese individuals, and full STR profiles could be generated using as little as 0.25 ng of genomic DNA. The method permitted clear discrimination of alleles and represents sensitive STR genotyping at a reduced cost.     

Improved Thermal and Reusability Properties of Xylanase by Genipin Cross-Linking to Magnetic Chitosan Particles

Enzymes are gradually increasingly preferred over chemical processes, but commercial enzyme applications remain limited due to their low stability and low product recovery, so the application of an immobilization technique is required for repeated use. The aims of this work were to produce stable enzyme complexes of cross-linked xylanase on magnetic chitosan, to describe some characteristics of these complexes, and to evaluate the thermal stability of the immobilized enzyme and its reusability. A xylanase was cross-linked to magnetite particles prepared by in situ co-precipitation of iron salts in a chitosan template. The effect of temperature, pH, kinetic parameters, and reusability on free and immobilized xylanase was evaluated. Magnetization, morphology, size, structural change, and thermal behavior of immobilized enzyme were described. 1.0?±?0.1 μg of xylanase was immobilized per milligram of superparamagnetic chitosan nanoparticles via covalent bonds formed with genipin. Immobilized xylanase showed thermal, pH, and catalytic velocity improvement compared to the free enzyme and can be reused three times. Heterogeneous aggregates of 254 nm were obtained after enzyme immobilization. The immobilization protocol used in this work was successful in retaining enzyme thermal stability and could be important in using natural compounds such as Fe₃O₄@Chitosan@Xylanase in the harsh temperature condition of relevant industries.

     

A dedicated NAA method to determine the neutron spectrum monitor elements Co,Au and Lu with high accuracy in alloyed wires and foils

A dedicated NAA calibration method was developed for the determination of the neutron spectrum monitor elements Co, Au and Lu in alloyed wires and foils, with an accuracy of better than 1%. The method does not require quantitative micropipetting for preparing the standards, and leads to vanishing errors caused by flux inhomogeneities and by differences in counting geometry and gamma attenuation. Its performance was tested by analysing various NIST, IRMM and RX aluminium-based materials with certified or specified Co, Au or Lu content.     

Synthesis of 3,3′-(1,6-hexanediyl)bis-pyrimidine derivatives and 3,4-dithia[6.6](1.3)pyrimidinophane

Several 3,3′-(1,6-hexanediyl)bis[6-methyl-2,4(1H,3H)-pyrimidinedione] derivatives ( 4a, 4b , and 4c ) were synthesized from 1,6-(hexanediyl)bis[6-methyl-2H-1,3-oxazine-2,4(3H)-dione] (3) . Compound 4c was converted to 6, which reacted with thiourea giving thiuronium salt 7 . 3,3′-(1,6-Hexanediyl)bis [1-(2-mercaptoethyl)-6-methyl-2,4(1H,3H)-pyrimidinedione] (9) was obtained by the hydrolysis of 7 , and then 9 was oxidized to 12,22-dimethyl-3,4-dithia[6.6] (1.3)-1,2,3,4-tetrahydro-2,4-dioxopyrimidinophane (10) .     

Diastereomeric Difference of the Self-Inclusion Complex of N(N′-Formyl-Phenylalanyl)-Deoxyamino-β-Cyclodextrin Caused by the Interaction between the Arm and the Rim of the Cavity

A complete assignment of proton resonances for N(N-formyl d-phenylalanyl)-deoxyamino--cyclodextrin (1d) was performed by means of 1D and 2D NMR,¹H–^1H-COSY, ¹H–^13C-COSY, TOCSYand NOESY spectroscopy. Based on 2D-NMR ROESY and circular dichroism spectroscopy, the conformation of 1d was determined; the phenyl group stays inside the distorted cyclodextrin (CyD) cavity forming a self-inclusion complex, which is almost the same as N(N-formyl l-phenylalanyl)-deoxyamino--CyD (1l). The remarkable diastereomeric difference was observed in the chemical shifts of H(5) and H(6) protons at the narrow rim of the CyD cavity and induced circular dichroism spectra. These results suggest the existence of hydrogen bonds between the hydroxyl group on CyD and the amide groups on the arms, which provides the difference in the molecular recognition properties.     

Stereoselectivity in the collision-activated reactions of gas phase salt complexes

The collision-activated dissociations (CAD) of gas phase salt complexes composed of chiral ions were studied in a quadrupole ion trap mass spectrometer. Because both partners in the salt are chiral, diastereomeric complexes can be formed (e.g., RR, RS). Two general types of complexes were investigated. In the first, the complex was composed of deprotonated binaphthol and a chiral bis-tetraalkylammonium dication. CAD of these complexes leads to the transfer of a proton or an alkyl cation to the binaphtholate leading to a singly-charged tetraalkylammonium cation. During CAD, diastereomeric complexes give significantly different product distributions indicating reasonable stereoselectivity in the process. In the second system, the complexes involved a peptide dianion and a chiral tetraalkylammonium cation. These systems may be viewed as very simple models for the interactions of peptides/proteins with small chiral molecules. Again, stereoselectivity was evident during CAD, but the extent was dependent on the nature of the peptide and not observable in some cases. To better understand the structural features needed to achieve stereoselectivity in gas phase salt complexes, representative transition states were modeled computationally. The results suggest that it is critical for the asymmetry of the nucleophile (i.e., anion) to be well represented in the vicinity of its reactive center.     

Experimental detection of proteolytic activity in a signal peptide peptidase of Arabidopsis thaliana

Background

The ubiquitin ligase COP1, COnstitutively Photomorphogenic 1, functions in many biological responses in mammalian cells, but its downstream pathway remains unclear.

Results

Here, we identified FIP200, a key regulator of mammalian autophagy, as a novel COP1-interacting protein by yeast two-hybrid screening. The interaction was confirmed by a GST-pulldown assay. Split-GFP analysis revealed that interaction between COP1 and FIP200 predominantly occurred in the cytoplasm and was enhanced in cells treated with UV irradiation. Different forms of FIP200 protein were expressed in cultured mammalian cells, and ectopic expression of COP1 reduced one of such forms.

Conclusions

These data suggest that COP1 modulates FIP200-associated activities, which may contribute to a variety of cellular functions that COP1 is involved in.     

Addition of 1,2- and 1,3-Dithiols to 2-alkoxypropenals - a New Method for the Production of Substituted Dithiacycloalkanes

The reaction of 2-alkoxypropenals with ethane-1,2-dithiols and propane-1,3-dithiols under various conditions was studied by ¹H NMR and chromato-mass spectrometry. Under kinetically controlled conditions at 20° in the absence of catalysts the addition of dithiols takes place according to the Markovnikov rule. The primary adducts are unstable and are quickly converted into the corresponding substituted 1,4-dithiacycloheptane or 1,4-dithiane. The latter in turn can be converted under the reaction conditions or at high temperature into a thiolane derivative. The reaction of 2-ethoxypropenal with a twofold excess of ethane-1,2-dithiol at 60°C in the presence of p-toluenesulfonic acid leads to 2-methyl-2,2'-bi(dithiolane)     

Molecule-Responsive Fluorescent Sensors of α-Helix Peptides Bearing α-Cyclodextrin, Pyrene and Nitrobenzene Units in Their Side Chains

-Helix peptides bearing one unit of -cyclodextrin (-CD), one unit of pyrene and one unit of nitrobenzene (NB) in their side chains have been designed and synthesized as novel molecule-responsive devices.In both the CD-peptides, -PR17 and -PL17, the NB unit is separated from the CD unit by two turns of the helix. Two reference peptides (PL17, and -P17,) have also been synthesized. The circular dichroism studies in the peptide absorption region (200–250 nm)of -PR17 and -PL17 suggestthat the CD-peptides form stable-helixstructures (83–77%), which was destabilized by accommodating guest molecules (e.g., n-pentanol) into the CD cavity. It suggests that formation of intramolecular host–guest(CD–NB) complex stabilized thehelical structure and exogenous guest molecule excluded the appending NB moiety from inside to outside of the CD cavity, thereby causing destabilization of the helical structure and increasing the random coil content. The ICD spectra of the peptides in the pyrene and nitrobenzene absorption region (250–40 nm) suggest that NB forms inclusion complex with CD. The fluorescence studies revealed that the fluorescence of the pyrene unit is quenched by the NB unit in -PR17 and -PL17. The fluorescence intensity increases with increasing guest concentration for the CD-peptides.This guest-responsiveenhancement in the fluorescence intensity can be explained in terms of increased distance between the pyrene and NB moieties, which is caused by exclusion of the NB moiety from the CD cavity by guest accommodation. Using the guest-responsive fluorescence quenching properties of the CD-peptides, we have obtained binding constants for various short chain alkanols. -PL17 has higher binding affinity to the guest molecules than its isomer, -PR17, indicating that the location of functional groups on the peptide scaffold is important in molecule detection.     

Cyanosilylation of α-butylthioacrolein

Cyanosilylation of α-butylthioacrolein with trimethylsilyl cyanide occurs as 1,2-addition. Concurrent rapid dimerization of α-butylthioacrolein occurred both in the presence and in the absence of H₂PtCl₆·6H₂O as a catalyst to give 2,5-dibutylthio-2,3-dihydro-4H-pyran-2-carbaldehyde, whose cyanosilylation afforded the corresponding cyanohydrin. The latter is prone to retrodiene degradation upon heating. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1418–1420, July, 1998.