A short and efficient synthesis of L-5,5,5,5',5',5'-hexafluoroleucine from N-Cbz-L-serine

[reaction: see text] 5,5,5,5',5',5'-Hexafluoroleucine (6), a fluorous analogue of leucine, is of considerable interest as a building block in the design of fluorous proteins and peptides. We report a short and efficient synthesis of 6, which is obtained from N-Cbz-L-serine (1) in 50% overall yield, 99% enantiomeric excess, and in multigram quantities. Key steps are addition of a serine-derived organozincate to hexafluoroacetone to construct the hexafluoroleucine side chain, followed by radical-mediated deoxygenation of the resulting tertiary alcohol.     

Development of a sugar-binding residue prediction system from protein sequences using support vector machine

Several methods have been proposed for protein–sugar binding site prediction using machine learning algorithms. However, they are not effective to learn various properties of binding site residues caused by various interactions between proteins and sugars. In this study, we classified sugars into acidic and nonacidic sugars and showed that their binding sites have different amino acid occurrence frequencies. By using this result, we developed sugar-binding residue predictors dedicated to the two classes of sugars: an acid sugar binding predictor and a nonacidic sugar binding predictor. We also developed a combination predictor which combines the results of the two predictors. We showed that when a sugar is known to be an acidic sugar, the acidic sugar binding predictor achieves the best performance, and showed that when a sugar is known to be a nonacidic sugar or is not known to be either of the two classes, the combination predictor achieves the best performance. Our method uses only amino acid sequences for prediction. Support vector machine was used as a machine learning algorithm and the position-specific scoring matrix created by the position-specific iterative basic local alignment search tool was used as the feature vector. We evaluated the performance of the predictors using five-fold cross-validation. We have launched our system, as an open source freeware tool on the GitHub repository (https://doi.org/10.5281/zenodo.61513).     

Low-dose radiation response of the p21WAF1/CIP1 gene promoter transduced by adeno-associated virus vector

In cancer gene therapy, restriction of antitumor transgene expression in a radiation field by use of ionizing radiation-inducible promoters is one of the promising approaches for tumor-specific gene delivery. Although tumor suppressor protein p53 is induced by low doses (< 1 Gy) of radiation, there have been only a few reports indicating potential utilization of a p53-target gene promoter, such as that of the p21 gene. This is mainly because the transiently transfected promoter of p53-target genes is not much sensitive to radiation. We examined the response of the p21 gene promoter to low-dose radiation when transduced into a human breast cancer cell line MCF-7 by use of recombinant adeno-associated virus (rAAV) vectors. It was shown that the p21 gene promoter transduced by rAAV vectors was more highly radiation-responsive than that transiently transfected by electroporation. A significant induction of the p21 gene promoter by radiation of low doses down to 0.2 Gy was observed. When cells were transduced with the p21 gene promoter-driven HSVtk gene by rAAV vector, they were significantly sensitized to repetitive treatment with low dose radiation (1 Gy) in the presence of the prodrug ganciclovir. It was therefore considered that the p21 gene promoter in combination with a rAAV vector is potentially usable for the development of a low-dose radiation-inducible vector for cancer gene therapy.     

In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3'-5' to 2'-5'

Deoxyribozymes that ligate RNA expand the scope of nucleic acid catalysis and allow preparation of site-specifically modified RNAs. Previously, deoxyribozymes that join a 5'-hydroxyl and a 2',3'-cyclic phosphate were identified by in vitro selection from random DNA pools. Here, the alternative strategy of in vitro evolution was used to transform the 8-17 deoxyribozyme that cleaves RNA into a family of DNA enzymes that ligate RNA. The parent 8-17 DNA enzyme cleaves native 3'-5' phosphodiester linkages but not 2'-5' bonds. Surprisingly, the new deoxyribozymes evolved from 8-17 create only 2'-5' linkages. Thus, reversing the direction of the DNA-mediated process from ligation to cleavage also switches the selectivity in forming the new phosphodiester bond. The same change in selectivity was observed upon evolution of the 10-23 RNA-cleaving deoxyribozyme into an RNA ligase. The DNA enzymes previously isolated from random pools also create 2'-5' linkages. Therefore, deoxyribozyme-mediated formation of a non-native 2'-5' phosphodiester linkage from a 5'-hydroxyl and a 2',3'-cyclic phosphate is strongly favored in many different contexts.     

Development of pyrrole-imidazole polyamide for specific regulation of human aurora kinase-A and -B gene expression

Pyrrole-imidazole polyamide (PIP) is a nuclease-resistant novel compound that inhibits gene expression through binding to the minor groove of DNA. Human aurora kinase-A (AURKA) and -B (AURKB) are important regulators in mitosis during the cell cycle. In this study, two specific PIPs (PIP-A and PIP-B) targeting AURKA and AURKB promoter regions were designed and synthesized, and their biological effects were investigated by several in vitro assays. PIP-A and PIP-B significantly inhibited the promoter activities, mRNA expression, and protein levels of AURKA and AURKB, respectively, in a concentration-dependent manner. Moreover, 1:1 combination treatment with both PIPs demonstrated prominent antiproliferative synergy (CI value [ED(50)] = 0.256) to HeLa cells as a result of inducing apoptosis-mediated severe catastrophe of cell-cycle progression. The novel synthesized PIP-A and PIP-B are potent and specific gene-silencing agents for AURKA and AURKB.     

A direct and efficient preparation of 1-phenyltetrazol-5-yl sulfides from alcohols

Treatment of primary or secondary alcohols with 1-phenyl-1(H)-tetrazole-5-thiol and [Me(2)NCHSEt](+) BF(4)(-) leads directly and cleanly to 1-phenyl-1(H)-tetrazol-5-yl sulfides.     

Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry

The human endothelial cell plasma membrane harbors two subdomains of similar lipid composition, caveolae and rafts, both crucially involved in various essential cellular processes like transcytosis, signal transduction and cholesterol homeostasis. Caveolin-enriched membranes, isolated by either cationic silica or buoyant density methods, were explored by comparing large series of two-dimensional (2-D) maps and subsequent identification of over 100 protein spots by matrix-assisted laser desorption/ionization (MALDI) peptide mass fingerprinting. Improved representation and identification of membrane proteins and valuable information on various post-translational modifications was achieved by the presented optimized procedures for solubilization, destaining and database searching/computing. Whereas the cationic silica purification yielded predominantly known endoplasmic reticulum residents, the cold-detergent method yielded a large number of known caveolae residents, including caveolin-1. Thus, a large part of this subproteome was established, including known (trans-)membrane, signal transduction and glycosyl phosphatidylinositol (GPI)-anchored proteins. Several predicted proteins from the human genome were isolated for the first time from biological samples, including SGRP58, SLP-2, C8ORF2, and XRP-2. These findings and various optimized procedures can serve as a reference to study the differential composition of endothelial cell caveolae and rafts, known to be involved in pathologies like cancer and cardiovascular disease.     

Highly efficient circulating tumor cell isolation from whole blood and label-free enumeration using polymer-based microfluidics with an integrated conductivity sensor

A novel microfluidic device that can selectively and specifically isolate exceedingly small numbers of circulating tumor cells (CTCs) through a monoclonal antibody (mAB) mediated process by sampling large input volumes (>/=1 mL) of whole blood directly in short time periods (<37 min) was demonstrated. The CTCs were concentrated into small volumes (190 nL), and the number of cells captured was read without labeling using an integrated conductivity sensor following release from the capture surface. The microfluidic device contained a series (51) of high-aspect ratio microchannels (35 mum width x 150 mum depth) that were replicated in poly(methyl methacrylate), PMMA, from a metal mold master. The microchannel walls were covalently decorated with mABs directed against breast cancer cells overexpressing the epithelial cell adhesion molecule (EpCAM). This microfluidic device could accept inputs of whole blood, and its CTC capture efficiency was made highly quantitative (>97%) by designing capture channels with the appropriate widths and heights. The isolated CTCs were readily released from the mAB capturing surface using trypsin. The released CTCs were then enumerated on-device using a novel, label-free solution conductivity route capable of detecting single tumor cells traveling through the detection electrodes. The conductivity readout provided near 100% detection efficiency and exquisite specificity for CTCs due to scaling factors and the nonoptimal electrical properties of potential interferences (erythrocytes or leukocytes). The simplicity in manufacturing the device and its ease of operation make it attractive for clinical applications requiring one-time use operation.     

Development of an enzyme-linked immunosorbent assay using specific monoclonal antibodies against theacrine and its application

Theacrine(1,3,7,9-tetramethyluric acid),a purine alkaloid similar to caffeine in its chemical structure,is isolated from edible Camellia assamica var.kucha and has various pharmacological activities including hypnotic effects,anti-depressant effects,anti-inflammatory and analgesic effects,and a protective effect against stress-provoked liver damage.A rapid and simple assay is required to quantify theacrine in biological samples for pharmacokinetic studies in small animals.This study aimed to establish an enzyme-linked immunosorbent assay(ELISA) for theacrine quantification in blood.Herein,we successfully obtained monoclonal antibodies(MAbs) against theacrine,MAbs C11B5,and developed an ELISA method for the fast determination of theacrine in mouse blood.The range for calibration of theacrine by ELISA was 0.156-100 μg mL~1.The half maximum inhibitory concentration(IC_(50)) value was1.55 μg mL~1.The ELISA method lays a good foundation for the further research.     

DABCO: an efficient promoter for the acetylation of carbohydrates and other substances under solvent-free conditions

A simple, mild and efficient solvent-free method for the acetylation of carbohydrates, and their partially protected derivatives, as well as non-carbohydrate substances in excellent yields in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) is described with the advantage of tolerance to various functional groups, short reaction time and ease of product isolation.     

Multicomponent synthesis of C-tethered bispyrazol-5-ols using CeO2 nanoparticles as an efficient and green catalyst

Research on Chemical Intermediates - CeO2 nanoparticles have been used as an efficient catalyst for the preparation of C-tethered bispyrazol-5-ols by pseudo five-component reaction of...     

Electrospray ionization mass spectrometry probing of formation and recognition of the G‐quadruplex in the proximal promoter of the human vascular endothelial growth factor gene

The formation of the G‐quadruplex of the vascular endothelial growth factor (VEGF) gene was probed by electrospray ionization mass spectrometry (ESI‐MS). It found that cations (K⁺ and NH), CH₃OH and pH influence significantly the formation of the G‐quadruplex structure. Additionally, a perylene derivative (P3) and polydatin (P4) have shown to be potential G‐quadruplex binding agents with structurally specific recognition. Copyright © 2010 John Wiley & Sons, Ltd.     

2',6'-Dimethylazobenzene as an efficient and thermo-stable photo-regulator for the photoregulation of DNA hybridization

The introduction of methyl groups into two ortho positions (2' and 6' positions) of the same benzene ring in an azobenzene remarkably raised both its photoregulation ability and the thermal stability of the cis-form.     

The use of tat and env sequences from human immunodeficiency virus 1 in phylogenetic epidemiological studies

Using nucleotide sequences from the first exon of the tat gene of the human immunodeficiency virus 1 (HIV-1), we tested the hypothesis that a Florida dentist (a common source) infected five of his patients in the course of dental procedures against the null hypothesis that the dentist and each individual of the dental group independently acquired the virus within the local community. This novel approach of analyzing the tat gene region was used because it may, in some circumstances, be more informative for phylogenetic epidemiology than the more commonly used C2-V3 envelope gene region. The first exon of the tat gene was polymerase chain reaction (PCR)-amplified and directly sequenced from uncultured peripheral blood mononuclear cells. Patient's sequences were compared with sequences from six HIV-1 infected heterosexual couples unrelated to the dentist or the five patients, but from the same general geographic area. In addition, a sixth infected dental patient, previously inferred to have acquired HIV-1 from a source other than the dentist, was included. Multiple phylogenetic analyses demonstrated that the sequences of the five patients were significantly more closely related to each other than to sequences of the controls. Our results using tat sequences, combined with envelope sequence data, strongly support a common phylogenetic epidemiological relationship among these five patients, and the HIV-1 infected dentist who treated them. Correct recovery of known epidemiological relationships among couples included in the analysis further strengthens this conclusion.     

The effective and specific isolation of antibodies from human serum by using thiophilic paramagnetic polymer beads

A rapid and effective method to specifically isolate immunoglobulin G (IgG) from human serum by thiophilic paramagnetic polymer beads was developed. The thiophilic paramagnetic beads were synthesized with vinyl acetate and divinylbenzene by microsuspension polymerization in the presence of magnetite nanoparticles. Divinylsulfone and 2-mercapto-benzothiazole were subsequently used to modify the surface of these beads, resulting in thiophilic particles that exhibited a high specificity to the antibodies in serum at low salt concentration. The adsorbed IgG was eluted by 0.8 M KCl and 72% of the IgG in the serum was recovered. The purity of the isolated IgG reached 98.4% and the bioactivity was fully maintained (>99%). The high efficiency, mild conditions and simplicity make this technology suitable for the economic purification of antibodies in a large scale.     

A simple and efficient approach to the synthesis of 1-phosphonated 5-amino-1-H-[1,2,4]-triazole from N-functionalized imidates

In this study, we describe a new and easy synthetic approach to variously substituted triazoles based on the reaction of imidates with phosphorylated hydrazine in good yields. A general mechanism of the reactions was also proposed. Characterization of the products was carried out by several analytical and spectroscopic tools including infrared and nuclear magnetic resonance spectroscopies (¹H, ¹³C NMR, ³¹P NMR).     

Development of a new method for the enantiomer specific determination of HBCD using an ion trap mass spectrometer

An alternative method for the enantiomer specific determination of hexabromocyclododecanes (HBCD) by LC-ESI-MS/MS using an ion trap analyser is proposed. The method is based on the formation of a chlorine adduct (m/z 676.6) of the (±)α-, (±)β-, and (±)γ-HBCD enantiomers and their further fragmentation into their stable quasi-molecular ion (m/z 640.6). In this way, problems related to the ion trap low mass cutoff and variable amounts of other adduct peaks in the samples are solved. Parameters affecting separation, ionisation and MS/MS detection were studied. Method performance was also evaluated: calibration curves were found linear from 20 to 400 pg μL⁻¹ for each enantiomer; detection limits ranged between 1.5 and 4.3 pg μL⁻¹; repeatability and reproducibility, expressed as relative standard deviation, were lower than 6% and 13%, respectively. The application to different types of spiked samples (pork meat, lean fish, and butter) pointed out the occurrence of matrix effects that could be solved by using labelled standards.