Phosphoramidites as Synthons for Polynucleotide Synthesis

Abstract

Methods for the rapid synthesis of DNA and RNA are described. The procedures involve using nucleoside phosphoramidites as synthons and silica as a polymeric support. Additionally, a novel reaction involving nucleoside O-alkyl methylphosphonothioates is described.     

Coating of titanium implant materials with thin polymeric films for binding the signaling protein BMP2

A fast and simple approach for immobilization using copolymers as interlayers is reported. The synthesized copolymers form stable self-assembled layers on implant materials like, e.g., titanium in a simple coating/drying/washing sequence and have functional groups which can bind proteins from an aqueous solution. The copolymer films have been characterized via ellipsometry and contact angle measurements and were tested for biocompatibility. An immunoassay was used to determine the amount of BMP2 and demonstrated an approximately 10-fold increase as compared to previously used self-assembled monolayers. A BMP2-responsive cell line with luciferase detection was used to determine the biological activity of the bound signaling protein.     

Kinetic study of the gas-phase reaction of OH with Br2

An experimental, temperature-dependent kinetic study of the gas-phase reaction of the hydroxyl radical with molecular bromine (reaction 1) has been performed by using a pulsed laser photolysis/pulsed-laser-induced fluorescence technique over a wide temperature range of 297-766 K, and at pressures between 6.68 and 40.29 kPa of helium. The experimental rate coefficients for reaction 1 demonstrate no correlation with pressure and exhibit a negative temperature dependence with a slight negative curvature in the Arrhenius plot. A nonlinear least-squares fit with two floating parameters of the temperature-dependent k(1)(T) data set using an equation of the form k(1)(T) = AT(n) yields the recommended expression k(1)(T) = (1.85 x 10(-9))T(-0.66) cm(3) molecule(-1) s(-1) for the temperature dependence of the reaction 1 rate coefficient. The potential energy surface (PES) of reaction 1 was investigated with use of quantum chemistry methods. The reaction proceeds through formation of a weakly bound OH...Br(2) complex and a PES saddle point with an energy below that of the reactants. Temperature dependence of the reaction rate coefficient was modeled by using the RRKM method on the basis of the calculated PES.     

Kinetics of the gas-phase reaction of OH with HCl

The reaction of hydroxyl radicals with hydrogen chloride (reaction 1) has been studied experimentally using a pulsed-laser photolysis/pulsed-laser-induced fluorescence technique over a wide range of temperatures, 298-1015 K, and at pressures between 5.33 and 26.48 kPa. The bimolecular rate coefficient data set obtained for reaction 1 demonstrates no dependence on pressure and exhibits positive temperature dependence that can be represented with modified three-parameter Arrhenius expression within the experimental temperature range: k1 = 3.20 x 10(-15)T0.99 exp(-62 K/T) cm3 molecule(-1) s(-1). The potential-energy surface has been studied using quantum chemical methods, and a transition-state theory model has been developed for the reaction 1 on the basis of calculations and experimental data. The model results in modified three-parameter Arrhenius expressions: k1 = 8.81 x 10(-16)T1.16 exp(58 K/T) cm3 molecule(-1) s(-1) for the temperature range 200-1015 K and k1 = 6.84 x 10(-19)T2.12 exp(646 K/T) cm3 molecule(-1) s(-1) for the temperature dependence of the reaction 1 rate coefficient extrapolation to high temperatures (500-3000 K). A temperature dependence of the rate coefficient of the Cl + H2O --> HCl + OH reaction has been derived on the basis of the experimental data, modeling, and thermochemical information.     

Synthesis and biochemical evaluation of phosphonoformate oligodeoxyribonucleotides

Phosphonoformate oligodeoxyribonucleotides were prepared via a solid phase synthesis strategy. The first step in the preparation of appropriate synthons was condensation of bis(N,N-diisopropylamino)phosphine and diphenylmethylsilylethyl chloroformate in the presence of sodium metal to yield formic acid, [bis(N,N-diisopropylamino)phosphino]-beta-(diphenylmethylsilylethyl) ester. The product of this reaction was then condensed with appropriately protected 2'-deoxynucleosides using 4,5-dicyanoimidazole to yield the 3'-O-phosphinoamidite reactive monomers. The exocyclic amines of cytosine, adenine, and guanine were protected with 9-fluorenylmethyloxycarbonyl, and oligodeoxyribonucleotides were synthesized on controlled pore glass using the hydroquinone-O,O'-diacetic acid linker. Synthons were sequentially added to this support using tetrazole as an activator, oxidized to phosphonoformate, and the transient 5'-protecting group was removed with acid. Following total synthesis of an oligomer, protecting groups were removed with TEMED.HF and products purified by HPLC. These analogues were resistant to nucleases, formed duplexes with complementary RNA (A-form), and, as chimeric oligomers containing phosphate at selected sites, stimulated RNase H1 activity.     

Challenges to computational quantum chemistry from contemporary advances in polyatomic molecular electronic spectroscopy

Molecular electronic spectroscopy featuring intramolecular proton transfer and twisted intramolecular charge transfer poses a whole new range of problems for computational quantum chemistry. The development of the four-level laser based on the intramolecular proton-transfer focuses on the subtleties of the interaction of the singlet and triplet electronic state manifolds of the two different tautomeric species. Examples are given of the sensitive variation of proton-transfer fluorescence with chemical substitution. A competing excitation channel is shown to exist when internal molecular torsion couples with sudden polarization to yield a twisted intramolecular charge transfer configuration. In such systems, three competing fluorescences can be observed. Several electronic puzzles will be presented that can provide fertile territory for quantum chemical computations. © 1993 John Wiley & Sons, Inc.     

Streamlined process for the chemical synthesis of RNA using 2'-O-thionocarbamate-protected nucleoside phosphoramidites in the solid phase

An improved method for the chemical synthesis of RNA was developed utilizing a streamlined method for the preparation of phosphoramidite monomers and a single-step deprotection of the resulting oligoribonucleotide product using 1,2-diamines under anhydrous conditions. The process is compatible with most standard heterobase protection and employs a 2'-O-(1,1-dioxo-1λ(6)-thiomorpholine-4-carbothioate) as a unique 2'-hydroxyl protective group. Using this approach, it was demonstrated that the chemical synthesis of RNA can be as simple and robust as the chemical synthesis of DNA.     

In vitro UPTAKE OF DICARBOXYLIC PORPHYRINS BY HUMAN ATHEROMA. KINETIC and ANALYTICAL STUDIES

Human atheromatous aorta segments as well as presumably disease-free control aorta were obtained at autopsy. They were incubated with solutions of various purified dicarboxylic porphyrins including hematoporphyrin (HP) and hydroxyethylvinyldeuteroporphyrin (HVD), and with solutions of Photofrin. Selective labelling of the atheroma was shown by macroscopic and microscopic observations of the characteristic porphyrin fluorescence associated with the atheromatous plaques. The time dependence of the uptake, monitored by absorption spectrophotometry or by high performance liquid chromatography, was inferred from the disappearance of the porphyrins in the incubation medium. Significant binding was observed in the absence of albumin or serum proteins. The uptake of HP was less than that of the more hydrophobic compounds HVD or Photofrin when these porphyrins were used alone. The presence of albumin or serum drastically reduces atheroma labelling. Some competition between HP and HVD for binding sites is also seen. The present results do indicate that hydrophobic porphyrins have an intrinsic affinity for atheroma and that they can be taken up through passive processes. Taking into account previous data on animal models (Photochem. Photobiol. (1989), 731-737), it appears however that, in vivo, interactions with proteins and pharmacokinetics will primarily determine plaque labelling.     

CELLULAR UPTAKE OF HYDROXYETHYLVINYLDEUTEROPORPHYRIN(HVD) AND PHOTOINACTIVATION OF CULTIVATED HUMAN LEUKEMIA (REH6) CELLS

Abstract— The in vitro incorporation of purified hydroxyethylvinyldeuteroporphyrin (HVD) into cells (Reh6) derived from an acute lymphocytic human leukemia is investigated using quantitative extraction techniques and fluorescence spectroscopy. A fast incorporation step (< 2 min) is characterized by its dependence on the porphyrin concentration in the incubation medium which suggests a saturation process. It is followed by a slower uptake, the rate of which linearly depends on the porphyrin concentration. No preferential uptake of aggregated form of HVD, which is shown to dimerize with an equilibrium constant of 9.7 × 10⁵ M ⁻¹, can be evidenced. As inferred from fluorescence spectra of cell suspensions and those of HVD dissolved in aqueous and micellar solutions as references, the porphyrin is mainly located in membrane structures and to a lower extent in cytoplasm. Cell photoinactivation does not depend on the incubation time but is only related to the intracellular porphyrin concentration.