Toward a microchip-based solid-phase extraction method for isolation of nucleic acids

A silica-based solid-phase extraction system suitable for incorporation into a microchip platform (nu-total analytical system; nu-TAS) would find utility in a variety of genetic analysis protocols, including DNA sequencing. The extraction procedure utilized is based on adsorption of the DNA onto bare silica. The procedure involves three steps: (i) DNA adsorption in the presence of a chaotropic salt, (ii) removal of contaminants with an alcohol/water solution, and (iii) elution of the adsorbed DNA in a small volume of buffer suitable for polymerase chain reaction (PCR) amplification. Multiple approaches for incorporation of this protocol into a microchip were examined with regard to extraction efficiency, reproducibility, stability, and the potential to provide PCR-amplifiable DNA. These included packing microchannels with silica beads only, generating a continuous silica network via sol-gel chemistry, and combinations of these. The optimal approach was found to involve immobilizing silica beads packed into the channel using a sol-gel network. This method allowed for successful extraction and elution of nanogram quantities of DNA in less than 25 min, with the DNA obtained in the elution buffer fraction. Evaluation of the eluted DNA indicated that it was of suitable quality for subsequent amplification by PCR.     

Prerequisites for peptidomic analysis of blood samples: II. Analysis of human plasma after oral glucose challenge -- a proof of concept

Mass spectrometric plasma analysis for biomarker discovery has become an exploratory focus in proteomic research: the challenges of analyzing plasma samples by mass spectrometry have become apparent not only since the human proteome organization (HUPO) has put much emphasis on the human plasma proteome. This work demonstrates fundamental proteomic research to reveal sensitivity and quantification capabilities of our Peptidomics technologies by detecting distinct changes in plasma peptide composition in samples after challenging healthy volunteers with orally administered glucose. Differential Peptide Display (DPD) is a technique for peptidomics studies to compare peptides from distinct biological samples. Mass spectrometry (MS) is used as a qualitative and quantitative analysis tool without previous trypsin digestion or labeling of the samples. Circulating peptides (< 15 kDa) were extracted from 1.3 mL plasma samples and the extracts separated by liquid chromatography into 96 fractions. Each fraction was subjected to MALDI MS, and mass spectra of all fractions were combined resulting in a 2D-display of > 2,000 peptides from each sample. Endogenous peptides that responded to oral glucose challenge were detected by DPD of pre-and post-challenge plasma samples from 16 healthy volunteers and subsequently identified by nESI-qTOF MS. Two of the 15 MS peaks that were significantly modulated by glucose challenge were subsequently identified as insulin and C-peptide. These results were validated by using immunoassays for insulin and C-peptide. This paper serves as a proof of principle for proteomic biomarker discovery down to the pM concentration range by using small amounts of human plasma.     

Unsymmetrical selenides from selenocyanates and methyl grignard

The addition of methyl Grignard to diethyl acetamido(cyanoselenobenzyl)malonates 3 and 4 at ?78° followed by hydrolysis yields the 3-(4-and 3-methylselenophenyl)alanines 1 and 2.     

Measurement of labile Cu in soil using stable isotope dilution and isotope ratio analysis by ICP-MS

Isotope dilution is a useful technique to measure the labile metal pool, which is the amount of metal in soil in rapid equilibrium (<7 days) with the soil solution. This is normally performed by equilibrating soil with a metal isotope, and sampling the labile metal pool by using an extraction (E value), or by growing plants (L value). For Cu, this procedure is problematic for E values, and impossible for L values, due to the short half-life of the ⁶⁴Cu radioisotope (12.4 h), which makes access and handling very difficult. We therefore developed a technique using enriched ⁶⁵Cu stable isotope and measurement of ⁶³Cu/⁶⁵Cu ratios by quadrupole inductively coupled plasma mass spectrometry (ICP-MS) to measure labile pools of Cu in soils using E value techniques. Mass spectral interferences in detection of ⁶³Cu/⁶⁵Cu ratios in soil extracts were found to be minimal. Isotope ratios determined by quadrupole ICP-MS compared well to those determined by high-resolution (magnetic sector) ICP-MS. E values determined using the stable isotope technique compared well to those determined using the radioisotope for both uncontaminated and Cu-contaminated soils.     

Purine acyclic nucleosides. Unambiguous synthesis of acyclovir via a furazano[3,4-d]pyrimidine

Acyclovir was synthesized in five steps from 7-formamido-5-methylthiofurazano[3,4-d]pyrimidine 2 . Alkylation of 2 with 2-(benzoyloxy)ethoxymethyl chloride, followed by reductive cleavage of the furazan ring gave 9-[[2-(benzoyloxy)ethoxy]methyl]-2-(methylthio)adenine 5 . Hydrolysis of the 6-amino group of 5 , followed by amination of 7 with ammonia gave 9-[(2-hydroxyethoxy)methyl]guanine ( 1 , acyclovir).     

Analysing fluorobenzoate tracers in groundwater samples using liquid chromatography-tandem mass spectrometry. A tool for leaching studies and hydrology

A sensitive LC-MS-MS method for the direct determination and quantification of 15 fluorobenzoic acids (FBAs) was developed. FBAs are used as conservative tracers for hydrological modelling of water flow and in studies of pesticides and other xenobiotic compounds. The use of FBAs is discussed in relation to other tracers (bromide, chloride, uranine). The method covers mono-substituted fluorobenzoic acid, difluorobenzoic acid, trifluorobenzoic acid, and tetrafluorobenzoic acid. The general detection limit in ground water was 1 microg/l using electrospray ionisation and 20 microg/l using atmospheric pressure chemical ionisation. Analysis time was less than 10 min, small sample volumes were needed and no clean-up was required.     

A practical synthesis of kifunensine analogues as inhibitors of endoplasmic reticulum alpha-mannosidase I

[reaction: see text] A practical synthesis of the potent class I alpha-mannosidase inhibitor kifunensine (1) beginning from the inexpensive and readily available starting material L-ascorbic acid (15) is described. The protected amino-alcohol ((2R,3R,4R,5R)-5-amino-2,3:4,6-diisopropylidenedioxyhexanol, 11) served as a key intermediate from which several N-1 substituted kifunensine analogues (including N-methyl, N-cyclohexyl, and N-bis(hydroxymethyl)methyl) and 2-desoxakifunensine analogues (including N-H and N-methyl) were prepared and screened for inhibition of human endoplasmic reticulum alpha-mannosidase I (ER Man I) and mouse Golgi alpha-mannosidase IA (Golgi Man IA). In addition, several pseudodisaccharide kifunensine analogues in which a mannose residue was tethered to N-1 of kifunensine via a two-, three-, or four-carbon linker and an affinity-bound kifunensine analogue were also prepared and evaluated for biological activity. While the synthesized N-1 kifunesine analogues were found to be less potent inhibitors of Class I alpha-mannosidases than kifuensine itself, the bis(hydroxymethyl)methylkifunensine analogue 6 was shown to selectively inhibit ER Man I over Golgi Man IA.     

Dynamic model for vibronic excitation in low energy atom-molecule collisions

Product state distributions from low energy He⁺N₂ and N⁺₂He collisions are presented. These data, obtained from collision-produced emission spectra, show severe deviations from Franck-Condon behavior which cannot be solely the result of molecular distortion arising from electrodynamic effects. A model based on consideration of the short-range interaction between the collision partners is proposed.     

The use of bis(diphenylphosphino)amines with N-aryl functionalities in selective ethylene tri- and tetramerisation

A systematic study was conducted on the Cr catalysed tri- and tetramerisation of ethylene using bis(diphenylphosphino)amine ligands with N-aryl functionality. This study revealed that the oligomerisation reaction product selectivity is primarily dependent on the structure and size of the N-aryl groups.

Addition of sufficient steric bulk to the N-phenyl group via ortho-alkyl substitution increased the combined 1-hexene and 1-octene selectivity (overall alpha selectivity) to above 82% at an overall 1-octene selectivity of 56%. The introduction of a single carbon spacer between the N-atom and the aryl-moiety, as well as the addition of branching on this carbon, resulted in further selectivity improvements, achieving an overall 1-octene selectivity of 64% and an overall alpha selectivity of 84%. This was obtained at catalyst productivities in excess of 1,000,000 g/g Cr/h.