Quantitation of ultraviolet-induced single-strand breaks using oligonucleotide chip

A simple, accurate and robust methodology was established for the direct quantification of ultraviolet (UV)-induced single-strand break (SSB) using oligonucleotide chip. Oligonucleotide chips were fabricated by covalently anchoring the fluorescent-labeled ssDNAs onto silicon dioxide chip surfaces. Assuming that the possibility of more than one UV-induced SSB to be generated in a small oligonucleotide is extremely low, SSB formation was investigated quantifying the endpoint probe density by fluorescence measurement upon UV irradiation. The SSB yields obtained based on the highly sensitive laser-induced fluorometric determination of fluorophore-labeled oligonucleotides were found to coincide well with that predicted from a theoretical extrapolation of the results obtained for plasmid DNAs using conventional agarose gel electrophoresis. The developed method has the potential to serve as a high throughput, sample-thrifty, and time saving tool to realize more realistic, and direct quantification of radiation and chemical-induced strand breaks. It will be especially useful for determining the frequency of SSBs or lesions convertible to SSBs by specific cleaving reagents or enzymes.     

Microchip gel electrophoresis with programmed field strength gradients for ultra-fast detection of canine T-cell lymphoma in dogs

This paper describes the applicability of microchip gel electrophoresis using a programmed field strength gradients (MGE-PFSG) method coupled with a polymerase chain reaction (PCR) for the ultra-fast diagnosis of canine T-cell lymphoma. The variable region in the T-cell receptor gamma (TCRgamma) gene from a T-cell lymphoma was used in PCR amplification. The contributions of the various parameters, including the effects of the molecular weight, concentration of the sieving matrix and field strength in MGE, were examined. 0.5% poly (ethyleneoxide) (PEO, M(r) 8000000) was used as the sieving matrix for the ultra-rapid separation of the amplified-PCR products (90 and 130-bp DNA fragments) from the PFSG at an effective length of 20mm in a glass microchip. The PCR products (90 and 130-bp DNA) of the T-cell lymphoma were analyzed within 41.7+/-0.1s, 15.5+/-0.2s and only 7.0+/-0.1s using a low-constant field strength, high-constant field strength and the PFSG, respectively. When 11 clinical samples were analyzed using the MGE-PFSG method, there was a 100% correlation with those obtained using conventional slab gel electrophoresis. The ultra-fast detection and rapid separation capabilities of MGE-PFSG make it an efficient tool for diagnosing T-cell lymphoma in clinical samples with high sensitivity.     

Macro- to nanoscale wear prevention via molecular adsorption

As the size of mechanical systems shrinks from macro- to nanoscales, surface phenomena such as adhesion, friction, and wear become increasingly significant. This paper demonstrates the use of alcohol adsorption as a means of continuously replenishing the lubricating layer on the working device surfaces and elucidates the tribochemical reaction products formed in the sliding contact region. Friction and wear of native silicon oxide were studied over a wide range of length scales from macro- to nanoscales using a ball-on-flat tribometer (millimeter scale), sidewall microelectromechanical system (MEMS) tribometer (micrometer scale), and atomic force microscopy (nanometer scale). In all cases, the alcohol vapor adsorption successfully lubricated and prevented wear. Imaging time-of-flight secondary ion mass spectrometry analysis of the sliding contact region revealed that high molecular weight oligomeric species were formed via tribochemical reactions of the adsorbed linear alcohol molecules. These tribochemical products seemed to enhance the lubrication and wear prevention. In the case of sidewall MEMS tests, the lifetime of the MEMS device was radically increased via vapor-phase lubrication with alcohol.     

Palladium nanoclusters supported on propylurea-modified siliceous mesocellular foam for coupling and hydrogenation reactions

This paper describes the synthesis, characterization and applications of palladium (Pd) nanoparticles supported on siliceous mesocellular foam (MCF). Pd nanoparticles of 2-3 nm and 4-6 nm were used in reactions involving molecular hydrogen (such as hydrogenation of double bonds and reductive amination), transfer hydrogenation of ketones and epoxides, and coupling reactions (such as Heck and Suzuki reactions). They successfully catalyzed all these reactions with excellent yield and selectivity. This heterogeneous catalyst was easily recovered by filtration, and recycled several times without any significant loss in activity and selectivity. The palladium leaching in the reactions was determined to be much less than the FDA-approved limit of 5 ppm. Furthermore, the catalyst can be stored and handled under normal atmospheric conditions. This immobilized catalyst allows for ease of recovery/reuse and minimization of waste generation, which are of great interest in the development of green chemical processes.     

Synthesis and activity of largazole analogues with linker and macrocycle modification

To characterize largazole's structural requirements for histone deacetylase (HDAC) inhibitory and antiproliferative activities, a series of analogues with modifications to the side chain or 16-membered macrocycle were prepared and biologically evaluated. Structure-activity relationships suggested that the four-atom linker between the macrocycle and octanoyl group in the side chain and the (S)-configuration at the C17 position are critical to repression of HDAC activity. However, the valine residue in the macrocycle can be replaced with alanine without significant loss of activity.     

Transient downregulation of protein O-N-acetylglucosaminylation by treatment of high-dose nicotinamide in human cells

Nicotinamide at millimolar concentrations affects cell survival in various conditions, and is being utilized therapeutically in many human diseases. However, the effect of an acute treatment of nicotinamide at such high dose on gene expression and cellular metabolism has rarely been determined previously. In this study, we found that levels of O-N-acetylglucosamin(O-GlcNAc)ylated proteins including Sp1 acutely decreased upon treatment of 10 mM nicotinamide. Concomitantly, Sp1 protein level decreased rapidly through accelerated proteasome-mediated proteolysis. Cotreatment of glucosamine or 2-deoxyglucose, which inhibits protein deGlcNAcylation, effectively blocked the decrease induced by nicotinamide. Interestingly, the decline in the levels of Sp1 and protein O- GlcNAcylation was only transient lasting for two days post treatment, and this pattern matched closely the rapid fluctuation of the cellular [NAD+]. Our results suggest a possible link between cellular nicotinamide metabolism and protein O-GlcNAcylation, and an existence of cellular [NAD+] homeostasis.     

Effect of ring torsion on intramolecular vibrational redistribution dynamics of 1,1'-binaphthyl and 2,2'-binaphthyl

The role of ring torsion in the enhancement of intramolecular vibrational energy redistribution (IVR) in aromatic molecules was investigated by conducting excitation and dispersed fluorescence spectroscopy of 1,1'-binaphthyl (1,1'-BN) and 2,2'-BN. The dispersed fluorescence spectra of 1,1'-BN in the origin region of S(1)-S(0) were well resolved, which presented 25-27 cm(-1) gaps of torsional mode in the ground state. The overall profile of the dispersed spectra of 1,1'-BN is similar to that of naphthalene. In contrast, the spectra of 2,2'-BN were not resolved due to the multitude of the active torsional modes. In both cases, dissipative IVR was observed to take place with a relatively small excess vibrational energy: 237.5 cm(-1) for 1,1'-BN and 658 cm(-1) for 2,2'-BN, which clearly shows that ring torsion efficiently enhances the IVR rate. Ab initio and density functional theory calculations with medium-sized basis sets showed that the torsional potential of 1,1'-BN has a very flat minimum over the range of torsional angles from ca. 60° to 120°, whereas that of 2,2'-BN showed two well-defined potential minima at ca. 40° and 140°, in resemblance to the case of biphenyl. In this work, we propose that aromatic molecules be classified into "strong" and "weak" torsional hindrance cases: molecules with strong hindrance case show shorter torsional progressions and more effective IVR dynamics than do those with weak hindrance.