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.     

A critical analysis of the effect of crosslinking on the linear viscoelastic behavior of styrene–butadiene rubber and other elastomers

The linear viscoelastic behavior in dynamic shear and tensile creep at temperatures from −30 to 70 °C is measured for an styrene–butadiene rubber (SBR) elastomer cured with dicumyl peroxide to crosslinking densities between 0 and 23.5 × 10⁻⁵ mol/cm³. The G′, G″, and tan δ isotherms are analyzed by time–temperature superposition (TTS), where the tan δ master curves are consistent with those of Mancke and Ferry. However, to achieve the TTS in the lightly crosslinked SBR systems, an anomalous vertical shift is required in the narrow temperature region from 10 to 30 °C. The vertical shift factor in this temperature region is not the standard from rubber elasticity. No anomalous behavior is detected in the equilibrium modulus, which is a linear function of temperature in accordance with the classical theory of rubber elasticity. In contrast to SBR, standard vertical shifts are required to effect TTS for uncrosslinked polybutadiene and an ethylene propylene diene monomer elastomer. © 2013 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013     

Conditions for the existence of weakly divergent bundles in plane-layered waveguides

We found conditions for the existence of weakly divergent bundles (WDB) of rays of different types in waveguides with a power-law dependence of the square of the refractive index. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika Vol. 42, No. 10, pp. 982–991, October, 1999.     

The influence of finite rates of temperature change in the creepT-jump experiment

Summary General equations for nonisothermal creep of a linear viscoelastic solid are presented. Both the time dependent strain and strain rate are predicted for an arbitrary temperature history. The creepT-jump experiment (imposition of a sudden temperature change on a creeping specimen) is analyzed using these equations in order to understand the influence of non-instantaneous temperature changes on the experimental observations. It is shown that an increase in the time required to impose the temperature change causes an increase in the activation energy,H _exp, determined via creepT-jump. This effect is most pronounced for materials with large activation energies. Appropriate extrapolation techniques can be used to obtain the result expected for an instantaneous temperature change. Verification of the theoretical prediction was obtained from isothermal and nonisothermal creep experiments on polymethylmethacrylate in the linear viscoelastic region. The activation energy for a nearly instantaneous temperature change was 43 ± 2 kcal/mol. As the rise time of the temperature change was increased to 600 seconds,H _exp increased to 70 ± 2 kcal/mol. The effects of the rate of temperature change on other aspects of the creepT-jump experiment were also found to be in keeping with the predictions of the nonisothermal linear theory.

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Zusammenfassung Es werden allgemeine Gleichungen für das nichtisotherme Kriechen eines linear-viskoelastischen Festkörpers abgeleitet. Sowohl die zeitabhängige Dehnung als auch die Dehngeschwindigkeit werden für eine beliebige Temperaturvorgeschichte vorausgesagt. Das Kriech-T-Sprung-Experiment, d.h. die Aufbringung einer plötzlichen Temperaturänderung bei einer Kriechprobe, wird mit diesen Gleichungen analysiert, um den Einfluß von kontinuierlichen Temperaturänderungen bei experimentellen Beobachtungen verständlich zu machen. Es wird gezeigt, daß eine Verlängerung der Zeitdauer zur Erzeugung der Temperaturänderung ein Anwachsen der AktivierungsenergieH _exp, verglichen mit derjenigen beim Kriech-T-Sprung, zur Folge hat. Dieser Effekt tritt am ausgeprägtesten bei Stoffen mit großen Aktivierungsenergien auf. Angepaßte Extrapolationsmethoden lassen sich anwenden, um das für eine plötzliche Temperaturänderung erwartete Ergebnis zu erhalten. Die theoretischen Voraussagen wurden mit Hilfe isothermer und nicht-isothermer Kriechexperimente an Polymethylmethacrylat im linearviskoelastischen Bereich verifiziert. Die Aktivierungsenergie für eine nahezu plötzliche Temperaturänderung ergab sich zu 43 ± 2 kcal/mol. Wenn das Zeitintervall für die Temperaturänderung auf 600 Sekunden erhöht wurde, stiegH _exp auf 70 ± 2 kcal/mol. Die Auswirkungen der Temperaturänderungsgeschwindigkeit bezüglich anderer Gesichtspunkte beim Kriech-T-Sprung-Experiment ergeben sich ebenso in Übereinstimmung mit den Voraussagen der nicht-isothermen linearen Theorie.

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With 15 figures     

A weight-function approach for determining watershed initial conditions for combustion waves

In many generic combustion models, one finds that a combustionwave will develop with a specific wave speed. However, thereare possible initial temperature profiles which do not evolveinto such waves, but rather die out to the ambient temperature.There can exist, in some models, a clear distinction betweenthose initial conditions that do evolve into combustion wavesand those that do not; this is sometimes referred to as thewatershed initial condition. When fuel consumption is consideredto be negligible, analytical methods can be used to obtain theexact watershed. In this paper, we consider the problem of determiningpseudo-watersheds and ascertaining the relationship betweenthese pseudo-watersheds and the exact watersheds. In the processa novel weight-function approach for infinite spatial domainsis developed.     

Rheological properties of poly(dimethylsiloxane) filled with fumed silica: II. Stress relaxation and stress growth

The steady-state viscosity, stress relaxation, and stress growth function were measured for a 3.0% by weight dispersion of fumed silica in poly(dimethylsiloxane); using a two-step shear rate history. For short rest times the stress growth function η⁺ increased monotonically towards steady-state, while at long rest times η⁺ exhibited large overshoot followed by a monotonic decrease to steady-state. For intermediate rest times η⁺ exhibited more complicated transient behaviour. The effect of both shear rates in the two-step shear-rate history on η⁺ have been studied, and the resulting rheological behaviour is discussed in terms of phenomenological microstructural models.     

Solid-phase synthesis and biochemical studies of O-boranophosphopeptides and O-dithiophosphopeptides

Signal transduction cascades maintain control over important cellular processes such as cell growth and differentiation by orchestrating protein phosphorylation and dephosphorylation. Specific control of these processes in vivo and in vitro can be achieved with peptide analogues that mimic the binding properties of phosphoproteins. We present here the solid-phase synthesis of two novel classes of phosphopeptide mimetics, O-boranophosphopeptides and O-dithiophosphopeptides, derivatized on tyrosine, serine, and threonine. The use of H-phosphonate and H-phosphonothioate monoesters containing the base labile 9-fluorenemethyl protecting group was key to the synthesis of both phosphopeptide mimetics. O-Boranophosphopeptides were synthesized by condensing O-(9-fluorenemethyl)-H-phosphonate to the peptide hydroxylic component (tyr, ser, or thr) followed by oxidation with borane complexes. Similarly, the synthesis of O-dithiophosphopeptides used the O-(9-fluorenemethyl)-H-phosphonothioate synthon and oxidation with elemental sulfur. Base elimination of the Fmol protecting group and cleavage from the solid support with concentrated ammonium hydroxide afforded the boranophosphopeptide and dithiophosphopeptide target compounds. Ac-YIIPLPG-NH2, having either dithiophosphoryl tyrosine or boranophosphoryltyrosine but no sequence specificity for Yersinia protein tyrosine phosphatase (PTP), was found to competitively inhibit this enzyme with KI values of 430 +/- 50 and 670 +/- 50 microM, respectively. In addition, both phosphopeptide analogues were resistant toward Yersinia PTP enzymatic hydrolysis. Under conditions (pH 8.0) where the phosphopeptide was rapidly dephosphorylated, the boranophosphopeptide hydrolyzed slowly (t1/2 = 15 h) and the dithiophosphopeptide was completely stable over 24 h.     

The effect of molecular weight on the rheological properties of poly(dimethylsiloxane) filled with fumed silica

The viscometric, stress relaxation, and stress growth rheological properties were measured for various molecular weight PDMS fluids filled with fumed silica. The stress growth function exhibited significant overshoot, when the continuous phase molecular weight was slightly greater than the entanglement molecular weight; however, significant overshoot peaks were not observed, when the continuous phase molecular weight was less than or much greater than the molecular weight between entanglements. The experimentally observed transient rheological properties are rationalized in terms of a molecular model, where interparticle interactions occur via entanglements of the polymer adsorbed on the silica surface. When the molecular weight of the adsorbed polymer is greater than the entanglement molecular weight, the strength of the interparticle interaction will increase substantially and the particle diffusivity will substantially decrease.     

Deformation induced evolution of mobility in PMMA

The stress relaxation response in the glassy state just below T_g was measured for poly(methylmethacrylate) following application of constant strain rate uniaxial tensile deformation at various locations on the stress–strain curve, including the yield and post‐yield region. The macroscopic mobility was determined from analysis of the relaxation response. Up to a factor of 3 decrease in relaxation time was observed with the fastest relaxation occurring in the post‐yield softening region. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010