Sequencing of antisense DNA analogues by capillary gel electrophoresis with laser-induced fluorescence detection

A method using capillary gel electrophoresis with laser-induced fluorescence detection is described which permits complete sequence determination of antisense DNA analogues of unknown sequence. This method, originally created as a tool to confirm the sequence of antisense oligonucleotides being developed as therapeutic drugs, utilizes data collected under a range of experimental conditions described by the Ogston model as applied to gel electrophoresis. A linear relationship independent of experimental conditions between the relative electrophoretic migration time and the oligonucleotide base number was observed and is shown to be consistent with a simplified version of this model and can be used to facilitate the sequence determination.     

The effect of alcohol structures on the interaction mode with the hexameric capsule of resorcin[4]arene

After more than a century of research on resorcin[4]arenes (1) it is clear that such systems form spontaneously [1(6)(H(2)O)(8)]-type hexameric capsules in wet, non-polar, organic solvents. However, the interactions of these hexameric capsules with alcohols are far from being solved. Here we provide the results of an extensive study on the interaction of different alcohols with the hexameric capsules of resorcin[4]arene 1a by focusing on the exchange of magnetization manifested in diffusion NMR measurements of such capsular systems. We found that some alcohols such as 2-octyl-1-dodecanol and 1-octadecanol do not interact with the hexamers of 1a, whereas other alcohols such as 3-ethyl-3-pentanol, 2-ethyl-1-butanol and more act as simple guests and are simply encapsulated in the hexamers. Others alcohols such as 3-pentanol, 2-methyl-1-butanol and others, are part of the hexameric structure where they can exchange magnetization with alcohols in the bulk. The bulkier alcohols, due to an increase of the chain length or in branching, have a higher tendency to be encapsulated rather than being part of the hexameric capsule superstructure. This study demonstrate the unique information that diffusion NMR spectroscopy can provide on supramolecular systems in solution and on the precaution that should be exercised when analyzing diffusion NMR data of such dynamic supramolecular capsules.     

Molecular length, monolayer density, and charge transport: lessons from Al-AlOx/alkyl-phosphonate/Hg junctions

A combined electronic transport-structure characterization of self-assembled monolayers (MLs) of alkyl-phosphonate (AP) chains on Al-AlOx substrates indicates a strong molecular structural effect on charge transport. On the basis of X-ray reflectivity, XPS, and FTIR data, we conclude that "long" APs (C14 and C16) form much denser MLs than do "short" APs (C8, C10, C12). While current through all junctions showed a tunneling-like exponential length-attenuation, junctions with sparsely packed "short" AP MLs attenuate the current relatively more efficiently than those with densely packed, "long" ones. Furthermore, "long" AP ML junctions showed strong bias variation of the length decay coefficient, β, while for "short" AP ML junctions β is nearly independent of bias. Therefore, even for these simple molecular systems made up of what are considered to be inert molecules, the tunneling distance cannot be varied independently of other electrical properties, as is commonly assumed.     

A combined method of neutron activation analysis and radiometric measurements for <Superscript>234</Superscript>U and <Superscript>238</Superscript>U determination in soil samples of low uranium concentration

A method that combines the use of non-destructive neutron activation analysis and high-resolution α spectrometry has been developed for determination of the activities of ²³⁴U and ²³⁸U in geological samples of low uranium content. The ²³⁸U content is determined by k₀-based neutron activation analysis, whereas the ²³⁴U/²³⁸U relationship is measured by α spectrometry after isolation and electrodeposition of the uranium extracted from a lixiviation with 6 M HCl. The main advantage of the method is the simplicity of the chemical operations, including the fact that the steps destined to assure similar chemical state for the tracer and the uranium species present in the sample are not necessary. The method was applied to soil samples from sites of the North Peru Coast. Uranium concentration range 3–40 mg/kg and the isotopic composition correspond to natural uranium, with about 10% uncertainty.     

RNA encapsidation by SV40-derived nanoparticles follows a rapid two-state mechanism

Remarkably, uniform virus-like particles self-assemble in a process that appears to follow a rapid kinetic mechanism. The mechanisms by which spherical viruses assemble from hundreds of capsid proteins around nucleic acid, however, are yet unresolved. Using time-resolved small-angle X-ray scattering (TR-SAXS), we have been able to directly visualize SV40 VP1 pentamers encapsidating short RNA molecules (500mers). This assembly process yields T = 1 icosahedral particles comprised of 12 pentamers and one RNA molecule. The reaction is nearly one-third complete within 35 ms, following a two-state kinetic process with no detectable intermediates. Theoretical analysis of kinetics, using a master equation, shows that the assembly process nucleates at the RNA and continues by a cascade of elongation reactions in which one VP1 pentamer is added at a time, with a rate of approximately 10(9) M(-1) s(-1). The reaction is highly robust and faster than the predicted diffusion limit. The emerging molecular mechanism, which appears to be general to viruses that assemble around nucleic acids, implicates long-ranged electrostatic interactions. The model proposes that the growing nucleo-protein complex acts as an electrostatic antenna that attracts other capsid subunits for the encapsidation process.     

A multi-shear perfusion bioreactor for investigating shear stress effects in endothelial cell constructs

Tissue engineering research is increasingly relying on the use of advanced cultivation technologies that provide rigorously-controlled cell microenvironments. Herein, we describe the features of a micro-fabricated Multi-Shear Perfusion Bioreactor (MSPB) designed to deliver up to six different levels of physiologically-relevant shear stresses (1-13 dyne cm(-2)) to six cell constructs simultaneously, during a single run. To attain a homogeneous fluid flow within each construct, flow-distributing nets photo-etched with a set of openings for fluid flow were placed up- and down-stream from each construct. Human umbilical vein endothelial cells (HUVECs) seeded in alginate scaffolds within the MSPB and subjected to three different levels of shear stress for 24 h, responded accordingly by expressing three different levels of the membranal marker Intercellular Adhesion Molecule 1 (ICAM-1) and the phosphorylated endothelial nitric oxide synthetase (eNOS). A longer period of cultivation, 17 d, under two different levels of shear stress resulted in different lengths of cell sprouts within the constructs. Collectively, the HUVEC behaviour within the different constructs confirms the feasibility of using the MSPB system for simultaneously imposing different shear stress levels, and for validating the flow regime in the bioreactor vessel as assessed by the computational fluid dynamic (CFD) model.     

The puzzle of contrast inversion in DNA STM imaging

DNA has been at the center of an imaging effort since the invention of the scanning tunneling microscope (STM). In some of the STM imaging reports the molecules appeared with negative contrast, i.e., "submerged" under the metal background and darker. We demonstrate the phenomenon of contrast inversion in DNA STM imaging by controlled and spontaneous contrast inversions and by the dependence of the DNA apparent height with respect to the surface on the imaging bias voltage. Using these characterizations, we formulate a model explaining the above phenomenon by resonant tunneling through virtual states in the vacuum between the STM tip and the DNA molecule.     

Propylene polymerization by C1‐symmetric {ONNO′}‐type salan zirconium complexes

The activities of C₁‐symmetric dibenzyl zirconium complexes of Salan ligands that bear a halo‐substituted phenolate ring and an alkyl‐substituted phenolate ring in propylene polymerization with methylaluminoxane as cocatalyst were studied. These {ONNO′}ZrBn₂‐type catalysts exhibited moderate‐to‐high activities and yielded polypropylene of low molecular weight. The degree of tacticity was found to depend on the steric bulk of the substituents on both phenolate rings and ranged from practically atactic to substantially isotactic (74–78% [mmmm] for polymerizations at room temperature by Lig⁵ZrBn₂). Hemi‐isotactic polypropylene was not obtained, despite the diastereotopicity of the two positions. The pattern of stereo errors was consistent with the enantiomorphic site control of propylene insertion typically observed for C₂‐symmetric catalysts and implied a facile site‐averaging mechanism. A regular 1,2‐insertion and a β‐H transfer to an incoming monomer correspond to the main propagation and termination processes, respectively. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

Synthesis, structure, and spectroscopy of phenylacetylenylene rods incorporating meso-substituted dipyrrin ligands

The synthesis, structure, and spectroscopic characterization of a series of phenylacetylenylene rodlike molecules containing dipyrromethene (dipyrrin) ligands are described. The combination of the phenylacetylenylene groups with the porphyrinogenic dipyrrin moieties results in a rich absorption spectroscopy for these compounds, although the fluorescence of the phenylacetylenylene moiety is quenched by presence of the dipyrrin chelator. The Cu(2+) and Fe(3+) complexes of these ligands have been prepared and three of these compounds have been structurally characterized by using single-crystal X-ray diffraction. Unlike other octahedral metal-dipyrrin complexes described to date, one of the iron complexes demonstrates ideal threefold symmetry in the solid-state. The elongated structure and high symmetry of these complexes suggests the use of these meso-substituted phenylacetylenylene ligands as an interesting class of extended, branched molecules for the construction of supramolecular architectures.     

Classification of chromatographic data using multidimensional polynomials

Summary A pattern recognition methodology has been developed for analysis of chromatographic data. The method uses a new class of multidimensional orthogonal polynomials developed by Cohen in conjunction with a supervised learning technique. The method is applicable to any chromatographic data for which classification into two or more categories is desired. The algorithm analyzes both elution times and peak areas. An application is shown for the analysis of organic acids in ascitic fluid obtained from patients with liver disorders. Classification of these patients for presence or absence of bacterial infection shows over ninety percent correct classification.