Fluorescence Analysis in Microarray Technology

Fluorescence has been the preferred choice for data quantification in biomedical microarray formats since their earliest days. As much as the formats have grown and evolved over the years, the methods in optical analysis have become ever more sophisticated and complex in order to produce more and better output. This review will provide an insight into the most common methods and the state-of-the-art of all areas in microarray fluorescence analysis. Starting with an overview on microarray formats with a focus on their demands on the readout, the most common and useful organic fluorescent stains are discussed before proceeding on to other approaches; the use of semiconductor nanocrystals (quantum dots), polymer and silica nanoparticles and fluorescent proteins. Ways to enhance the intrinsically low signal on biochips have become increasingly important as they offer a sound approach towards the detection of low concentration sample content. The three main categories are presented: amplification using DNA, enzymes, and dendrimers. As much diversity as on the microarrays themselves can be found at the detection device. Standard optical microarray detectors, and non-standard methods using fluorescence anisotropy, fluorescence lifetime imaging (FLIM) and fluorescence resonance energy transfer (FRET), and their advantages and disadvantages are discussed.     

Assessing weak intramolecular donor-acceptor interactions using 1H-117Sn J-HMQC spectroscopy

It is demonstrated that long-range nJ(1H,117Sn) coupling constants down to 0.3 Hz, can be accurately quantified from non-linear fitting of the sine modulation of the associated 1H-117Sn correlation cross-peak intensities sampled as a function of the heteronuclear antiphase coherence preparation time in the 1H-117Sn J-HMQC pulse sequence. The contribution of additional, undesired modulations is illustrated and assessed using the product operator formalism, and is traced back to contributions that arise from miss-setting of the wandering 180 degrees pulse angle in the constant time period. The power of the method and its use in the characterization of weak intramolecular donor-acceptor interactions are illustrated by the determination of long-range nJ(1H,117Sn) coupling constants of bis[3-(dimethylamino)propyl]tin derivatives, [Me2N(CH2)3]2SnR2 (', R = Me; 3, R = Ph; 4, R = t-Bu). By comparing these with the values found for the corresponding bis(4-methylpentyl)tin derivatives, [Me2CH(CH2)3]2SnR2 (2', R = Me; 3', R = Ph), which lack such interactions, the use of long-range coupling constants to detect intramolecular donor-acceptor interactions is evaluated. It is concluded that nJ(1H,117Sn) couplings up to six bonds through an organic carbon chain can be quantified, whether donor-acceptor interactions are present or not. Furthermore, evidence is presented that, when two scalar coupling pathways co-exist, the pathway involving an intramolecular donor-acceptor interaction can have opposite sign, thus decreasing the overall coupling constant to a value smaller than that actually measured in the absence of a donor-acceptor interaction, where only one coupling pathway is active. There is nevertheless clear numerical value discrimination in the series of compounds investigated between long-range couplings in derivatives without weak intramolecular donor-acceptor interactions and those where such interactions can exist.     

Molecular gradients: an efficient approach for optimizing the surface properties of biomaterials and biochips

A variety of molecular gradients of alkanethiols with the structure HS-(CH(2))(m)-X (m = 15; X = COOH, CH(2)NH(2), or CH(3)) and oligo(ethylene glycol)-terminated alkanethiols with the structures HS-(CH(2))(15)-CO-NH-Eg(n) (n = 2, 4, or 6), HS-(CH(2))(15)-CO-NH-Eg(2)-(CH(2))(2)-NH-CO-(CH(2))(4)-biotin, and HS-(CH(2))(15)-CO-NH-Eg(6)-CH(2)-COOH were prepared on polycrystalline gold films. These gradients were designed to serve as model surfaces for fundamental studies of protein adsorption and immobilization phenomena. Ellipsometry, infrared spectroscopy, and X-ray photoelectron spectroscopy, operating in scanning mode, were used to monitor the layer composition, gradient profiles, tail group conformation, and overall structural quality of the gradient assemblies. The gradient profiles were found to be 4-10 mm wide, and they increased in width with increasing difference in molecular complexity between the thiols used to form the gradient. The oligo(ethylene glycol) thiols are particularly interesting because they can be used to prepare so-called conformational gradients, that is, gradients that display a variation in oligo(ethylene glycol) chain conformation from all trans on the extreme Eg(2,4) sides, via an amorphous-like phase in the mixing regimes, to helical at the extreme Eg(6) sides. We demonstrate herein a series of experiments where the above gradients are used to evaluate nonspecific binding of the plasma protein fibrinogen, and in agreement with previous studies, the highest amounts of nonspecifically bound fibrinogen were observed on all-trans monolayers, that is, on the extreme Eg(2,4) sides. Moreover, gradients between Eg(2) and a biotinylated analogue have been prepared to optimize the conditions for the immobilization of streptavidin. Ellipsometry and infrared spectroscopy reveal high levels of immobilization over a fairly broad range of compositions in the gradient regime, with a maximum between 50 and 60% of the biotinylated analogue in the monolayer. A pI gradient composed of (NH(3)(+)/COO(-))-terminated thiols was also prepared and evaluated with respect to its ability to separate differently charged proteins, pepsin, and lysozyme, on a solid surface.     

Crystal structure, oxidation state and magnetism of La1.2Sr2.4RuO7: a new member of the [A2O][AnBn−1O3n] series of hexagonal perovskites

Single crystals of the new compound La_1.2Sr_2.4RuO₇, an oxide related to the hexagonal perovskites, were grown from a BaCl₂ flux. The structure was solved by single crystal X-ray diffraction. La_1.2Sr_2.4RuO₇ crystallizes in the space group with a=5.760(1) Å and c=18.273(3) Å. It is one of the rare examples of oxides with isolated RuO₆-octahedra. The structure consists of alternating layers of RuO₆-octahedra and trigonal (La,Sr)O₆-prisms. These prisms are capped by one additional oxygen ion, which occupies a distorted position within the (La,Sr)O₆-layers. La_1.2Sr_2.4RuO₇ is the second member of the general [A₂O][A_nB_n−1O_3n] family of hexagonal perovskites with n=2 and the first ruthenate possessing this structure. XANES investigations, bond valence sum calculations and magnetic measurements show that ruthenium takes the oxidation state +5. Although the ruthenium ions have quite long distances, a medium strong antiferromagnetic interaction between these paramagnetic centers was observed.     

1H detection in MAS solid-state NMR spectroscopy of biomacromolecules employing pulsed field gradients for residual solvent suppression

In this communication, we demonstrate the feasibility of 1H detection in MAS solid-state NMR for a microcrystalline, uniformly 2H,15N-labeled sample of a SH3 domain of chicken alpha-spectrin, using pulsed field gradients for suppression of water magnetization. Today, B0 gradients are employed routinely in solution-state NMR for coherence order selection and solvent suppression. We suggest to use gradients to purge water magnetization which cannot be suppressed using conventional water suppression schemes. The achievable gain in sensitivity for 1H detection is in the order of 5 compared to the 15N detected version of the experiment (at a MAS rotation frequency of 13.5 kHz). We expect that this labeling concept which achieves high sensitivity due to 1H detection, in combination with the possibility to measure long range 1H-1H distances as we have shown previously, to be a useful tool for the determination of protein structures in the solid state.     

Conformation and Crystal Structure of Dipyrrinones with Oxindole Components

 Pyrrole α-aldehydes (2-formyl-4,5-dimethyl-1H-pyrrole and 2-formyl-N-methylpyrrole) condense readily at C(3) of indolin-2-ones to give dipyrrinone analogs, such as (3Z)-[(4,5-dimethylpyrrol-2-yl)-methylidenyl]-indolin-2-one and (3E)-[(1-methylpyrrol-2-yl)-methylidenyl]-indolin-2-one. ¹H-NMR NOE analyses and X-ray crystallography confirm the syn-(Z) configuration for the former and the syn-(E) configuration for the latter. The former is stabilized by intramolecular hydrogen bonding. Molecular mechanics calculations of the latter indicate no energy difference between the syn and anti conformations.     

Identification of amber and imitations by near infrared reflection spectroscopy

Imitations of amber have been prepared since a long time, but the number of imitations is increasing since modern polymers are available. At present, many imitations are based on a few synthetic polymers and even experts have some problems in distinguishing between real and falsed amber without destruction of the material. IR-Spectroscopy or pyrolysis combined with gas chromatography/mass spectrometry are very efficient methods in identifying amber and imitations but these methods need a sample preparation. By means of near infrared reflection spectroscopy it is possible to identify amber and imitations without any sample preparation in a short time. Optimization of the method and the application are discussed.     

The solvent extraction of Cu(II), Ni(II), and Co(II) with diacetyl-mono-(2-quinolylhydrazone)

Summary A semi-automatic microliter sample injector with an 8-way motor-driven rotary valve was constructed for a conventional pneumatic nebulizer. After a 40-l sample was injected into an injection tee with a micro-syringe, nebulization and flushing the sample pathway with water followed by argon were automatically executed. An automatic peak detector/integrator was employed in each channel of a three-channel spectrometer for simultaneous multielement analysis. The relative standard deviation of the peak height for 1g Zr/ml was 1.7% and measuring time of one sample was about 1 min. Detection limits were 2 to 6 times higher than those in continuous feeding.

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Halbautomatische Injektion von Mikroliter-Proben in ein induktiv gekoppeltes Plasma zwecks simultaner Multielementanalyse

Zusammenfassung Ein halbautomatischer Injektor für Mikroliterproben mit einem motorgetriebenen 8-Weg-Ventil für ein konventionelles Vernebelungsgerät wurde konstruiert. Nachdem eine 40-l-Probe mit einer Mikroinjektionsspritze in ein Injektions-T-Stück eingeführt ist, erfolgt automatisch Vernebelung, dann Spülung des Probenweges zunächst mit Wasser, dann mit Argon. Ein automatischer Spitzen-Detektor/Integrator in jedem der drei Kanäle des Spektrometers ermöglicht die gleichzeitige Multielementanalyse. Die rel. Standardabweichung der Spitzenhöhe für 1g Zr/ml betrug 1,7%, die Zeit für die Messung einer Probe ungefähr eine Minute. Die Nachweisgrenzen sind 2- bis 6mal höher als bei kontinuierlicher Zugabe.

     

Synthesis and structure of the metallic K6Tl17: a layered tetrahedral star structure related to that of Cr3Si

The title compound, the Tl-richest in the K-Tl system, has been synthesized in Ta containers via direct reaction of the elements at 400 degrees C followed by quenching to room temperature and subsequent annealing at 150 degrees C for 4 weeks. It crystallizes in the orthorhombic space group Cccm (No. 66) with a = 16.625(1) A, b = 23.594(2) A, c = 15.369(2) A (22 degrees C), and Z = 8. Two different Tl(12) units consisting of augmented tetrahedral stars are condensed into layers of such tetrahedra, and further Tl(2) dumbbells and the potassium cations also interconnect the stars and layers into a three-dimensional network. The former anionic Tl(8) subunits clearly resemble those in the heteroatomic 3-D structure of cubic Cr(3)Si before their augmentation with bridging atoms. The compound is metallic (rho(270) = 22.6 micro omega x cm, alpha = 0.0023 K(-)(1)) and shows Pauli-like paramagnetic susceptibility (chi(296) = 1.1 x 10(-4) emu/mol). EHTB calculations illustrate the importance of Tl p-orbital bonding, the positive Tl-Tl overlap populations up to E(F), and greater strengths of the Tl-Tl bonding between and about the surface of the augmented Tl(12) units. Cations between the thallium layers play specific and important roles in the structure.