A novel phosphoramidite method for automated synthesis of oligonucleotides on glass supports for biosensor development

Two protocols for functionalization of glass supports with hexaethylene glycol (HEG)-linked oligonucleotides were developed. The first method (standard amidite protocol) made use of the 2-cyanoethyl-phosphoramidite derivative of 4,4′-dimethoxytrityl-protected HEG. This was first coupled to the support by standard solid-phase phosphoramidite chemistry followed by extension with a thymidylic acid icosanucleotide. Stepwise addition of the linker phosphoramidite graduated at 1% (relative to the total sites available) perstep at 50°C resulted in an optimal yield of immobilized oligonucleotides at a density of 2.24 × 10¹⁰ strands/mm². This observed loading maximum lies well below the theoretical maximum loading owing to nonspecific adsorption of HEG on the glass and subsequent blocking of reactive sites. Surface loadings as high as 3.73 × 10¹⁰/mm² and of excellent sequence quality were achieved with a reverse amidite protocol. The support was first modified into a 2-cyanoethyl-N,N-diisopropylphosphoramidite analog followed by coupling with 4,4′-dimethoxytrityl-protected HEG. This protocol is conveniently available when using a conventional DNA synthesizer. The reverse amidite protocol allowed for control of the surface loading at values suitable for subsequent analytical applications that make use of immobilized oligonucleotides as probes for selective hybridization of sample nucleic acids of unknown sequence and concentration.     

On the dissolution processes of Na2I+ and Na3I2+ with the association of water molecules: mechanistic and energetic details

The sequential association energies for one through six water molecules clustering to Na(2)I(+), as well as one and two water molecules clustering to Na(3)I(2)(+), are measured. The association energies show a pairwise behavior, indicating a symmetric association of water molecules to the linear Na(2)I(+) and Na(3)I(2)(+) ions. This pairwise behavior is well reproduced by Density Functional Theory (DFT) calculations. DFT calculations also suggest that a significant separation of charge for the Na-I ion pair occurs when four or more water molecules cluster to a single sodium center. Two different solvent-separated ion pairs have been identified with the DFT calculations. Experiments also show that the dissolution processes, loss of a neutral NaI unit, occurs when six or more water molecules have been added to Na(2)I(+) cluster. However, one or two water molecules are able to detach an NaI unit from the Na(3)I(2)(+) cluster. The difference in solubility of the Na(2)I(+) and Na(3)I(2)(+) ions is due to the difference in the energies required to lose an NaI unit from these two species. The experiment also confirms that the loss of a neutral NaI unit, instead of an Na(+) ion, occurs during the dissolution processes of Na(3)I(2)(+). The microsolvation schemes proposed to explain our experimental observations are supported by DFT and phase space theory (PST) calculations.     

Dynamics of a triphenylene discotic molecule,HAT6, in the columnar and isotropic liquid phases

Discotic molecules have planar, disklike polyaromatic cores that can self-assemble into "molecular wires". Highly anisotropic charge transfer along the wires arises when there is sufficient intermolecular overlap of the pi-orbitals of the molecular cores. Discotic materials can be applied in molecular electronics, field-effect transistors, and-recently with record quantum efficiencies-photovoltaics (Schmidt-Mende, L.; Fechtenk?tter, A.; Müllen, K.; Moons, E.; Frien, R. H.; MacKenzie, J. D. Science 2001, 293, 1119). A combination of quasielastic neutron scattering (QENS) measurements with molecular dynamics simulations on the discotic molecule hexakis(n-hexyloxy)triphenylene (HAT6) shows that the dynamics of the cores and tails of discotic molecules are strongly correlated. Core and tail dynamics are not separated, the system being characterized by overall in-plane motion, on a time scale of 0.2 ps, and softer out-of-plane motions at 7 ps. Because charge transfer between the molecules is on similar time scales, these motions are relevant for the conducting properties of the materials. Both types of motion are dominated by van der Waals interactions. Small-amplitude in-plane motions in which the disks move over each other are almost entirely determined by tail/tail interactions, these also playing an important role in the out-of-plane motion. The QENS measurements reveal that these motions are little changed by passing from the columnar phase to the isotropic liquid phase, just above the clearing temperature. The model of four HAT6 molecules in a column reproduces the measured QENS spectrum of the liquid phase, suggesting that correlations persist within the liquid phase over about this number of disks.     

Intact size-selected Au(n) clusters on a TiO2(110)-(1 x 1) surface at room temperature

Experiments in which mass-selected gold clusters were deposited on a surface have found that the catalytic properties depend strongly on cluster size. However, these experiments have not established definitively that the clusters maintain their size after deposition. We report here work in which we deposit low kinetic energy, mass-selected Aun+ (n = 1-8) clusters on a rutile TiO2(1 x 1) surface and use ultrahigh vacuum scanning tunneling microscopy (UHV-STM) to determine their size and shape.     

The stereoselective synthesis of aziridine analogues of diaminopimelic acid (DAP) and their interaction with dap epimerase

Aziridine analogues of diaminopimelic acid (DAP) have been prepared stereoselectively for the first time and evaluated as inhibitors of DAP epimerase. (2R,3S,3'S)-3-(3'-Aminopropane)aziridine-2,3'-dicarboxylate was synthesised and shown to be a reversible inhibitor of DAP epimerase with an IC(50) value of 2.88 mM. (2S,4S)- and (2S,4R)-2-(4-Amino-4-carboxybutyl)aziridine-2-carboxylic acid (ll-azi-DAP and dl-azi-DAP ) were made as pure diastereomers, and both were shown to be irreversible inhibitors of DAP epimerase. ll-Azi-DAP selectively binds to Cys-73 of the enzyme active site whereas dl-azi-DAP binds to Cys-217 via attack of sulfhydryl on the methylene of the inhibitor aziridine ring. These observations are consistent with the two base mechanism proposed for the epimerization of ll-DAP and meso-DAP by DAP epimerase.     

Chemiluminescence from the oxidation of urea and ammonia with hypobromite and N-bromosuccinimide

The spectral distribution for the chemiluminescent oxidation of ammonia with hypobromite is significantly different to that for the oxidation of ammonia with N-bromosuccinimide. Therefore, in contrast to the assumptions of several authors, the action of N-bromosuccinimide is not solely derived from the in situ formation of hypobromite. Neither the oxidation of urea with hypobromite nor the oxidation of urea with N-bromosuccinimide involves an initial hydrolysis of urea to ammonia in the alkaline solution. However, these two reactions lead to a common emitter. The addition of xanthene dyes, such as dichlorofluorescein, enhance the chemiluminescence intensity by energy transfer to the efficient fluorophore, but reaction between the sensitiser and hypobromite can result in a significant increase in the background signal. A list of potential interferences has been compiled; particular attention was paid to guanidino compounds, as the chemiluminescence accompanying the oxidation of this functional group has not been previously discussed.     

Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design

It has been suggested from QSAR data (P. D. Edwards, D. J. Wolanin, D.A. Andisik and M. W. Davis, J. Med. Chem., 1995, 38, 76) that the inhibition of elastase by peptidyl alpha-ketoheterocyclic inhibitors can occur in two ways, the less potent inhibitors forming a non-bonded Michaelis complex and the more potent set a covalently bonded enzyme-substrate intermediate. We report QM/MM studies of both binding and reactivity that confirm these findings, showing that the activity of the least potent set of inhibitors correlates with the calculated binding energy, and that of the more potent set correlates with the stability of the intermediate. These calculations show that QM/MM methods can be successfully employed to understand complicated structure-activity relationships and might be employed in the design and assessment of new inhibitors.     

Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation

Summary A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H₁-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys²⁰⁰, Thr²⁰³ and Asn²⁰⁷, for which a functional role in binding has been proposed. The most favourable results were obtained for the interaction between Hist and the Lys²⁰⁰/Asn²⁰⁷ pair. Therefore, Lys²⁰⁰ was subsequently mutated and converted to an alanine, resulting in a 50-fold decrease of H₁-receptor stimulation by histamine. Altogether, the data suggest that the Lys²⁰⁰/Asn²⁰⁷ pair is important for activation of the H₁-receptor by histamine. In contrast, analogues of 2-PhHist seem to belong to a distinct subclass of histamine agonists and an alternative mode of binding is proposed in which the 2-phenyl ring binds to the same receptor location as one of the aromatic rings of classical histamine H₁-antagonists. Subsequently, the binding modes of the agonists Hist, 2-MeHist and 2-PhHist and the H₁-antagonist cyproheptadine were evaluated in three different seven--helical models of the H₁-receptor built in homology with bacteriorhodopsin, but using three different alignments. Our findings suggest that the position of the carboxylate group of Asp¹¹⁶ (TM3) within the receptor pocket depends on whether an agonist or an antagonist binds to the protein; a conformational change of this aspartate residue upon agonist binding is expected to play an essential role in receptor stimulation.Abbreviations 2-MeHist 2-methylhistamine - 2-PEA 2-pyridyl-ethylamine - 2-PhHist 2-phenylhistamine - CHO Chinese hamster ovary - E_int interaction energy - E_str strain energy - GES global energy structure - gpH₁R guinea pig H₁-receptor - GPCR G-protein coupled receptor - Hist histamine - N proximal nitrogen - N tele nitrogen - TM transmembrane domain - WT wild type     

Kinetic and mechanistic studies of the reaction of a range of bases and metal-hydroxo complexes with the phosphonate ester 2,4-dinitrophenyl ethyl methylphosphonate in aqueous solution

The base hydrolysis and spontaneous water hydrolysis of the phosphonate ester 2,4-dinitrophenyl ethyl methylphosphonate (DNPEMP) has been studied in detail and the activation parameters for these processes determined. The catalytic effect of a series of 19 oxygen and nitrogen bases and metal hydroxo complexes has been studied. The Brønsted plot of pK versus logkN has a slope (β) of 0.47, which is fairly typical for phosphate and phosphonate esters. alpha-Effect nucleophiles such as 2-iodosobenzoate, hypochlorite and the hydroperoxide ion (HO-2) exhibit enhanced reactivity, as does fluoride ion and the bifunctional metal complex [Cu(tmen) (OH2)(OH)]+ (tmen = N,N,N',N',-tetramethylethylenediamine). Reactions involving these species appear to take place by a nucleophilic pathway, while the other oxygen and nitrogen bases act as general base catalysts. The solvent deuterium isotope effect for Et3N catalysis, kH2O/kD2O=1.3, is consistent with general base catalysis. The mechanisms of these reactions are discussed in detail.     

Molecular and crystal structures of ruthenium and osmium arene clusters

The molecular and crystal structures of a number of ruthenium and osmium clusters of nuclearity between three and six containing arene fragments such as C₆H₆, C₆H₃Me₃, C₆H₄Me₂ and C₆H₅Me have been investigated. Attention has been focused on the relationship between the terminal ( ⁶-coordination) and face-capping ( ₃: ²: ²: ²-coordination) bonding modes. Empirical packing potential energy calculations have been employed to investigate the intermolecular organization in the crystal. It has been shown that the arene fragments in mono-arene clusters form ribbons, while in bis-arene clusters graphitic-like interactions throughout the crystal are established. The factors controlling the ease of arene reorientational motion in the solid state has also been investigated in relation to the shape, size and geometry of the molecules and of their interlocking modes.