A review on immobilised aptamers for high throughput biomolecular detection and screening

The discovery of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has led to the generation of aptamers from libraries of nucleic acids. Concomitantly, aptamer-target recognition and its potential biomedical applications have become a major research endeavour. Aptamers possess unique properties that make them superior biological receptors to antibodies with a plethora of target molecules. Some specific areas of opportunities explored for aptamer-target interactions include biochemical analysis, cell signalling and targeting, biomolecular purification processes, pathogen detection and, clinical diagnosis and therapy. Most of these potential applications rely on the effective immobilisation of aptamers on support systems to probe target species. Hence, recent research focus is geared towards immobilising aptamers as oligosorbents for biodetection and bioscreening. This article seeks to review advances in immobilised aptameric binding with associated successful milestones and respective limitations. A proposal for high throughput bioscreening using continuous polymeric adsorbents is also presented.     

Visible light-mediated atom transfer radical addition via oxidative and reductive quenching of photocatalysts

Herein, the development of visible light-mediated atom transfer radical addition (ATRA) of haloalkanes onto alkenes and alkynes using the reductive and oxidative quenching of [Ir{dF(CF(3))ppy}(2)(dtbbpy)]PF(6) and [Ru(bpy)(3)]Cl(2) is presented. Initial investigations indicated that the oxidative quenching of photocatalysts could effectively be utilized for ATRA, and since that report, the protocol has been expanded by broadening the scope of the reaction in terms of the photocatalysts, substrates, and solvents. In addition, further modifications of the reaction conditions allowed for the efficient ATRA of perfluoroalkyl iodides onto alkenes and alkynes utilizing the reductive quenching cycle of [Ru(bpy)(3)]Cl(2) with sodium ascorbate as the sacrificial electron donor. These results signify the complementary nature of the oxidative and reductive quenching pathways of photocatalysts and the ability to predictably direct reaction outcome through modification of the reaction conditions.     

Multiquantum vibrational excitation of NO scattered from Au(111): quantitative comparison of benchmark data to ab initio theories of nonadiabatic molecule-surface interactions

Surface phenomena: measurements of absolute probabilities are reported for the vibrational excitation of NO(v=0→1,2) molecules scattered from a Au(111) surface. These measurements were quantitatively compared to calculations based on ab?initio theoretical approaches to electronically nonadiabatic molecule-surface interactions. Good agreement was found between theory and experiment (see picture; T(s) =surface temperature, P=excitation probability, and E=incidence energy of translation).     

Rapid computation of intermolecular interactions in molecular and ionic clusters: self-consistent polarization plus symmetry-adapted perturbation theory

A method that we have recently introduced for rapid computation of intermolecular interaction energies is reformulated and subjected to further tests. The method employs monomer-based self-consistent field calculations with an electrostatic embedding designed to capture many-body polarization (the "XPol" procedure), augmented by pairwise symmetry-adapted perturbation theory (SAPT) to capture dispersion and exchange interactions along with any remaining induction effects. A rigorous derivation of the XPol+SAPT methodology is presented here, which demonstrates that the method is systematically improvable, and moreover introduces some additional intermolecular interactions as compared to the more heuristic derivation that was presented previously. Applications to various non-covalent complexes and clusters are presented, including geometry optimizations and one-dimensional potential energy scans. The performance of the XPol+SAPT methodology in its present form (based on second-order intermolecular perturbation theory and neglecting intramolecular electron correlation) is qualitatively acceptable across a wide variety of systems-and quantitatively quite good in certain cases-but the quality of the results is rather sensitive to the choice of one-particle basis set. Basis sets that work well for dispersion-bound systems offer less-than-optimal performance for clusters dominated by induction and electrostatic interactions, and vice versa. A compromise basis set is identified that affords good results for both induction and dispersion interactions, although this favorable performance ultimately relies on error cancellation, as in traditional low-order SAPT. Suggestions for future improvements to the methodology are discussed.     

In situ infrared spectroscopic study of brucite carbonation in dry to water-saturated supercritical carbon dioxide

In geologic carbon sequestration, whereas part of the injected carbon dioxide will dissolve into host brine, some will remain as neat to water saturated supercritical CO(2) (scCO(2)) near the well bore and at the caprock, especially in the short term life cycle of the sequestration site. Little is known about the reactivity of minerals with scCO(2) containing variable concentrations of water. In this study, we used high-pressure infrared spectroscopy to examine the carbonation of brucite (Mg(OH)(2)) in situ over a 24 h reaction period with scCO(2) containing water concentrations between 0% and 100% saturation, at temperatures of 35, 50, and 70 °C, and at a pressure of 100 bar. Little or no detectable carbonation was observed when brucite was reacted with neat scCO(2). Higher water concentrations and higher temperatures led to greater brucite carbonation rates and larger extents of conversion to magnesium carbonate products. The only observed carbonation product at 35 °C was nesquehonite (MgCO(3)·3H(2)O). Mixtures of nesquehonite and magnesite (MgCO(3)) were detected at 50 °C, but magnesite was more prevalent with increasing water concentration. Both an amorphous hydrated magnesium carbonate solid and magnesite were detected at 70 °C, but magnesite predominated with increasing water concentration. The identity of the magnesium carbonate products appears strongly linked to magnesium water exchange kinetics through temperature and water availability effects.     

Kinetics of the O + ICN reaction

The kinetics of the O + ICN reaction was studied using a relative rate method, with O + C(2)H(2) as the competing reaction. Carbon monoxide products formed in the competing reaction and subsequent secondary chemistry were detected as a function of reagent ICN pressure to obtain total rate constants for the O + ICN reaction. Analysis of the experimental data yields rate constants of k(1) = (3.7 ± 1.0 to 26.2 ± 4.0) × 10(-14) cm(3) molecule(-1) s(-1) over the total pressure range 1.5-9.5 Torr. Product channel NCO + I, the only bimolecular exothermic channel of the reaction, was investigated by detection of N(2)O in the presence of NO and found to be insignificant. An ab initio calculation of the potential energy surface (PES) of the reaction at the CCSD(T)/CEP-31G//DFT-B3LYP/CEP-31G level of theory was also performed. The pathways leading to bimolecular product channels are kinetically unfavorable. Formation and subsequent stabilization of an ICNO adduct species appears to dominate the reaction, in agreement with the experimentally observed pressure dependent rate constants.     

Copper-mediated difluoromethylation of aryl and vinyl iodides

Selectively fluorinated molecules are important as materials, pharmaceuticals, and agrochemicals, but their synthesis by simple, mild, laboratory methods is challenging. We report a straightforward method for the cross-coupling of aryl and vinyl iodides with a difluoromethyl group generated from readily available reagents to form difluoromethylarenes and difluoromethyl-substituted alkenes. The reaction of electron-neutral, electron-rich, and sterically hindered aryl and vinyl iodides with the combination of CuI, CsF and TMSCF(2)H leads to the formation of difluoromethyl-substituted products in high yield with good functional group compatibility. This transformation is surprising, in part, because of the prior observation of the instability of CuCF(2)H.     

Low-load rotor-synchronised Hahn-echo pulse train (RS-HEPT) 1H decoupling in solid-state NMR: factors affecting MAS spin-echo dephasing times

Transverse dephasing times T(2)' in spin-echo MAS NMR using rotor-synchronised Hahn-echo pulse-train (RS-HEPT) low-load (1)H decoupling are evaluated. Experiments were performed at 300 and 600 MHz for (13)CH-labelled L-alanine and (15)NH(delta)-labelled L-histidine.HCl.H(2)O, together with SPINEVOLUTION simulations for a ten-spin system representing the crystal structure environment of the (13)CH carbon in L-alanine. For 30 kHz MAS and nu(1)((1)H) = 100 kHz at 300 MHz, a RS-HEPT T(2)' value of 17 +/- 1 ms was obtained for (13)CH-labelled L-alanine which is approximately 50% of the XiX T(2)' value of 33 +/- 2 ms. Optimum RS-HEPT decoupling performance is observed for a relative phase of alternate RS-HEPT pi-pulses, Deltaphi = phi'- phi, between 40 and 60 degrees . For experiments at 600 MHz and 30 kHz MAS with (13)CH-labelled L-alanine, the best RS-HEPT (nu(1)((1)H) = 100 kHz) T(2)' value was 3 times longer than that observed for low-power continuously applied sequences with nu(1)((1)H) < or =40 kHz, i.e. corresponding to the same average power dissipated in the probe. A marked improvement in RS-HEPT (1)H decoupling is observed for increasing MAS frequency: at 55.6 kHz MAS, a best RS-HEPT T(2)' value of 34 +/- 5 ms was recorded for (13)CH-labelled L-alanine. Much improved RS-HEPT broadband performance was also observed at 55.6 kHz MAS as compared to 30 kHz MAS.     

Mass spectral analysis and imaging of tissue by ToF-SIMS—The role of buckminsterfullerene, C60, primary ions

Recent developments in desorption/ionisation mass spectrometry techniques have made their application to biological analysis a realistic and successful proposition. Developments in primary ion source technology, mainly through the advent of polyatomic ion beams, have meant that the technique of secondary ion mass spectrometry (SIMS) can now access the depths of information required to allow biological imaging to be a viable option.Here the role of the primary ion C₆₀⁺ is assessed with regard to molecular imaging of lipids and pharmaceuticals within tissue sections. High secondary ion yields and low surface damage accumulation are demonstrated on both model and real biological samples, indicating the high secondary ion efficiency afforded to the analyst by this primary ion when compared to other cluster ion beams used in imaging. The newly developed 40 keV C₆₀⁺ ion source allows the beam to be focused such that high resolution imaging is demonstrated on a tissue sample, and the greater yields allow the molecular signal from the drug raclopride to be imaged within tissue section following in vivo dosing.The localisation shown for this drug alludes to issues regarding the chemical environment affecting the ionisation probability of the molecule; the importance of this effect is demonstrated with model systems and the possibility of using laser post-ionisation as a method for reducing this consequence of bio-sample complexity is demonstrated and discussed.