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.     

Evaluation of a complete HPLC solvent optimization system involving piece-wise quadratic modelling

Summary Interpretive methods are accepted to give the best possible results for selectivity optimization in HPLC. However the methods are very complex, and most work so far has been detailed academic studies. This paper describes an evaluation of a complete integrated system incorporating peak labelling, modelling of retention behaviour and calculation of response surfaces, with particular emphasis on the retention modelling. The peak labelling section has been discussed previously.A piece-wise quadratic function is investigated for the modelling of retention times across an isoeluotropic plane to effect selectivity optimization in HPLC. This requires 10 data-points on the isoeluotropic plane. The predicted global optimum and local optima are evaluated by comparison of calculated and experimental retention data, for a nine component sample. Seven interstitial points, distributed across the whole plane between the data-points, are similarly evaluated for a related sample. The typical error (in retention time) is less than 2%, often 1%, and the maximum error is 4.2%. At the global optimum the error was found be less than 1.3% for all 9 peaks.     

Automated multi-attribute method sample preparation using high-throughput buffer exchange tips

Rationale

The multi-attribute method (MAM) has become a valuable mass spectrometry (MS)-based tool that can identify and quantify the site-specific product attributes and purity information for biotherapeutics such as monoclonal antibodies (mAbs) and fusion molecules in recent years. As we expand the use of the MAM at various stages of drug development, it is critical to enhance the sample preparation throughput without additional chemical modifications and variability.

Methods

In this study, a fully automated MAM sample preparation protocol is presented, where rapid desalting in less than 15 minutes is achieved using miniaturized size-exclusion chromatography columns in pipette tips on an automated liquid handler. The peptide samples were analyzed using an electrospray ionization (ESI) orbitrap mass spectrometer coupled to an ultra-high-performance liquid chromatography (UHPLC) system with a dual column switching system.

Results

No significant change was observed in product attributes and their quantities compared with manual, low-artifact sample preparation. The sample recovery using the buffer exchange tips was greatly enhanced over the manual spin cartridges while still demonstrating excellent reproducibility for a wide variety of starting sample concentrations. Unlike a plate desalting system, the individual columns provide flexibility in the number of samples prepared at a time and sample locations within plates.

Conclusions

This automated protocol enables the preparation of up to 96 samples with less “at-bench” time than the manual preparation of a smaller batch of samples, thereby greatly facilitating support of process development and the use of the MAM in quality control.

     

Morphology-dependent stimulated Raman scattering (MDSRS)

A novel non-linear Raman spectroscopic technique, which can be used to characterize the chemical composition of the interface region of volatile aerosol particles, is described. The technique is morphology-dependent stimulated Raman scattering (MDSRS). We discuss the phenomenology behind this new optical probe, and present experimental results which show that this technique can be used as quantitative spectroscopic tool. We outline the potential application of MDSRS to in situ gas—aerosol kinetics and dynamics studies.     

Enhancing selectivity in oxidation catalysis with sol-gel nanocomposites

Valuable organic compounds such as alpha-hydroxy acids are easily synthesised with relevant selectivity enhancement using a sol-gel hydrophobized nanostructured silica matrix doped with the organocatalyst TEMPO: A materials science based synthetic route which cannot be achieved via classical homogeneous synthesis.     

Direct Electrochemical Investigations of 17-Electron Complexes of CpM(CO)(3)(*) (M = Mo, W, and Cr)

Photolysis of complexes of the type M(2)(CO)(6)(RC(5)H(4))(2) (where M = W, Mo, Cr and R = H (Cp) or CH(3) (Cp')) leads to the production of short lived 17-electron radicals. Direct electrochemical characterization of these intermediates has been achieved using a technique known as photomodulated voltammetry (PMV). The results from PMV analysis are in excellent agreement with literature estimates for CpMo(CO)(3)(*) and CpCr(CO)(3)(*). However, CpW(CO)(3)(*) is found to be shifted oxidatively 115 mV relative to previous literature estimates. The change in the value for the tungsten complex changes previous estimates to the bond dissociation energy for tungsten metal hydrides by 3.0 +/- 0.9 kcal/mol. Lifetime information on the radicals is also reported based on the phase shift of the electrochemical signal observed by PMV under limiting current conditions.     

Preparation and spectroscopic properties of 2-benzothiazolyl araldehyde hydrazones

Notwithstanding its tendency toward air oxidation in solution, 2-hydrazinobenzothiazole I reacted with aromatic aldehydes in ethanol to give the corresponding hydrazones III-XV in high yields and analytical purity. In related examples, acylation took place under similar conditions to produce hydrazides XVI-XX . The near-infrared bands of the absorption spectra of the araldehyde hydrazones have been associated with charge transfer and appeared to correlate with structural elements of the compounds in a way suggesting that the charge transfer was intermolecular.     

Molecular ordering and 2D conductivity in ultrathin poly(3-hexylthiophene)/gold nanoparticle composite films

This paper reports the first comparison of the structure and electrical conductivity properties of spin cast (SC) and Langmuir-Schaeffer (LS) films of regioregular poly(3-hexylthiophene) (P3HT). In addition, the effect of incorporating highly monodisperse Au nanoparticles (NPs), with a core diameter of approximately 5 nm, into SC and LS P3HT films is described. A detailed picture of molecular organization in the films has been obtained using ultraviolet-visible absorption spectroscopy, atomic force microscopy, field-emission scanning electron microscopy, X-ray diffraction, and X-ray reflectivity. Film morphology was correlated with pseudo-two-dimensional conductivity measured using scanning electrochemical microscopy, with P3HT in the semiconducting regime. It was found that SC films, which were slightly thicker than those formed with the LS technique, exhibited greater organization. This resulted in an order of magnitude higher lateral conductivity for the SC films. Inclusion of Au NPs (50 wt %) into both SC and LS films resulted in the formation of uniform and relatively flat (rms roughness approximately 1 nm) composite films. Surprisingly, the addition of NPs did not disrupt the characteristic crystal structure found for the native P3HT films. The effect of Au NPs on film lateral conductivity was found to be determined by the distribution of Au NPs within the polymer, which varied significantly between SC and LS films. Whereas Au NPs aggregated into hexagonally packed clusters in SC films, NPs in LS films were predominantly uniformly distributed between the lamella bilayer. It was found that, while the inclusion of Au NPs caused the lateral conductivity to decrease in SC films, in LS films, the lateral conductivity increased by a factor of 2.     

A simple and general chiral silicon Lewis acid for asymmetric synthesis: highly enantioselective [3+2] acylhydrazone-enol ether cycloadditions

A highly diastereo- and enantioselective [3 + 2] acylhydrazone-enol ether cycloaddition mediated by a simple chiral silane Lewis acid is described. The reactions are highly practical, as demonstrated by a larger scale (5 g of the hydrazone) reaction in which the product was obtained after recrystallization in 93% yield and 99% ee. Evidence for a stepwise mechanism and a model for the asymmetric induction are presented, as well.     

Trypsin activity assay in substrate-specific one- and two-dimensional gels: a powerful method to separate and characterize novel proteases in active form in biological samples

To separate and identify the proteases, a substrate-specific, sensitive assay in sodium dodecyl sulfate (SDS)-polyacrylamide gels after two-dimensional (2-D) electrophoresis has been developed. This method allows simultaneous determination of protease cleavage specificity, molecular weight, isoelectric point, and if necessary, amino acid sequencing. After isoelectric focusing in immobilized pH gradient (IPG) strips (pH 6-11) (first dimension), trypsin was electrophoresed in 12% SDS polyacrylamide gels (second dimension) copolymerized with Boc-Gln-Ala-Arg-MCA (4-methyl-coumaryl-7-amide). The gels were washed in cold 2.5% Triton X-100 and water, and incubated in assay buffer (6.3 mM Bicine, 100 mM NaCl). Trypsin cleavage of the peptide-MCA generated fluorescent 7-amino-4-methyl-coumarin. In 1-D gels, as low as 500 pg trypsin could be detected and trypsin band volumes correlated linearly with the amounts of trypsin (R(2) = 0.999). In 2-D gels, the lowest amount of trypsin detected was 1 ng. The linear regression of spot volume and loading amount was still good (R(2) = 0.974). To optimize renaturation conditions, 5x5 min washes with 2.5% Triton X-100 and water, respectively, gave the strongest band volume. For fluorescence development, an assay buffer at pH 9 was the best; incubation at 37 degrees C for 30 min was sufficient. The method has application for identifying novel proteases as it does not rely on antibodies.