The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs

The stability and replication of DNA containing self-pairs formed between unnatural nucleotides bearing benzofuran, benzothiophene, indole, and benzotriazole nucleobases are reported. These nucleobase analogues are based on a similar scaffold but have different hydrogen-bond donor/acceptor groups that are expected to be oriented in the duplex minor groove. The unnatural base pairs do not appear to induce major structural distortions and are accommodated within the constraints of a B-form duplex. The differences between these unnatural base pairs are manifest only in the polymerase-mediated extension step, not in base-pair stability or synthesis. The benzotriazole self-pair is extended with an efficiency that is only 200-fold less than a correct natural base pair. The data are discussed in terms of available polymerase crystal structures and imply that further modifications may result in unnatural base pairs that can be both efficiently synthesized and extended, resulting in an expanded genetic alphabet.     

REMGa3Ge and RE3Ni3Ga8Ge3 (M = Ni, Co; RE = rare-earth element): new intermetallics synthesized in liquid gallium. X-ray, electron, and neutron structure determination and magnetism

New quaternary intermetallic phases REMGa(3)Ge (1) (RE = Y, Sm, Tb, Gd, Er, Tm; M = Ni, Co) and RE(3)Ni(3)Ga(8)Ge(3) (2) (RE = Sm, Gd) were obtained from exploratory reactions involving rare-earth elements (RE), transition metal (M), Ge, and excess liquid Ga the reactive solvent. The crystal structures were solved with single-crystal X-ray and electron diffraction. The crystals of 1 and 2 are tetragonal. Single-crystal X-ray data: YNiGa(3)Ge, a = 4.1748(10) A, c = 23.710(8) A, V = 413.24(2) A(3), I4/mmm, Z = 4; Gd(3)Ni(3)Ga(8)Ge(3), a = 4.1809(18) A, c = 17.035(11) A, V = 297.8(3) A(3), P4/mmm, Z = 1. Both compounds feature square nets of Ga atoms. The distribution of Ga and Ge atoms in the REMGa(3)Ge was determined with neutron diffraction. The neutron experiments revealed that in 1 the Ge atoms are specifically located at the 4e crystallographic site, while Ga atoms are at 4d and 8g. The crystal structures of these compounds are related and could be derived from the consecutive stacking of disordered [MGa](2) puckered layers, monatomic RE-Ge planes and [MGa(4)Ge(2)] slabs. Complex superstructures with modulations occurring in the ab-plane and believed to be associated with the square nets of Ga atoms were found by electron diffraction. The magnetic measurements show antiferromagnetic ordering of the moments located on the RE atoms at low temperature, and Curie-Weiss behavior at higher temperatures with the values of mu(eff) close to those expected for RE(3+) free ions.     

Pd(II)-catalyzed conversion of styrene derivatives to acetals: impact of (-)-sparteine on regioselectivity

[reaction: see text] Pd[(-)-sparteine]Cl(2) catalyzes the formation of dialkyl acetals from styrene derivatives with Markovnikov regioselectivity. The substrate scope of this reaction has been investigated, and initial mechanistic studies indicate that the reaction proceeds through an enol ether intermediate and a Pd-hydride.     

The effect of magnetic fields on the electrodeposition of iron

The effect of a uniform magnetic field with flux density up to 1 T on the electrodeposition of Fe from sulphate electrolyte has been investigated under different field configurations relative to the electrode surface. Voltammetric and chronoamperometric experiments have been carried out coupled with an electrochemical quartz crystal microbalance for in situ mass change measurements. The structure and morphology of the deposited films were determined by scanning electron microscopy, atomic force microscopy and X-ray diffraction measurements. Results show that, when the magnetic field is applied parallel to the electrode surface, the limiting current density and the deposition rate are increased due to the magnetohydrodynamic effect. The nucleation process is also affected in parallel configuration; the current density of the maximum on the chronoamperograms is decreased, and an additional nucleation step might be observed. This effect is attributed to the hydrodynamic response of the electrochemical system. No significant influence on the electrochemical reaction was observed when a magnetic field was applied perpendicular to the electrode. But in this configuration, the morphology of deposited layers is changed by the magnetic field. The morphology changes are discussed. No effect of the magnetic field on the crystallographic structure was observed.     

Polymers of Carbonic Acid, 31. Cyclic Polycarbonates by Hydrolytic Polycondensation of Bisphenol‐A Bischloroformate

The hydrolytic polycondensation of bisphenol‐A bischloroformate in NaOH/CH₂Cl₂ was studied using triethylamine as the catalyst. Reaction conditions were optimized towards high molar masses. The isolated polycarbonates were characterized by means of SEC and MALDI‐TOF mass spectrometry. The fraction of cyclic polycarbonates strongly increased with higher molecular weights and in the best sample only cycles were detectable (up to 50 000 Da). The largest cycles can compete with cyclic DNS of microorganisms.     

Rational Design of a Humanized Glucagon‐Like Peptide‐1 Receptor Agonist Antibody

Bovine antibody BLV1H12 possesses a unique “stalk–knob” architecture in its ultralong heavy chain CDR3, allowing substitutions of the “knob” domain with protein agonists to generate functional antibody chimeras. We have generated a humanized glucagon‐like peptide‐1 (GLP‐1) receptor agonist antibody by first introducing a coiled‐coil “stalk” into CDR3H of the antibody herceptin. Exendin‐4 (Ex‐4), a GLP‐1 receptor agonist, was then fused to the engineered stalk with flexible linkers, and a Factor Xa cleavage site was inserted immediately in front of Ex‐4 to allow release of the N‐terminus of the fused peptide. The resulting clipped herceptin–Ex‐4 fusion protein is more potent in vitro in activating GLP‐1 receptors than the Ex‐4 peptide. The clipped herceptin–Ex‐4 has an extended plasma half‐life of approximately four days and sustained control of blood glucose levels for more than a week in mice. This work provides a novel approach to the development of human or humanized agonist antibodies as therapeutics.     

REDUCED PHOTOINACTIVATION OF 10-DODECYL ACRIDINE ORANGE-SENSITIZED YEAST CELLS AT HIGH FLUENCE RATES MEASUREMENTS AND COMPUTER SIMULATIONS

Abstract-During the development of a photodamage cell sorter several photosensitizers were tested for their ability to photoinactivate more than 90% of the sensitized cells after a brief irradiation with a fluence of 10 kJ/m². In pilot experiments, yeast cells sensitized with 10-dodecyl acridine orange (DAO) were effectively photoinactivated after receiving a fluence of 10 kJ/m² delivered in 8 s. However, when the same fluence was delivered in 3 μ s during passage through a focused laser beam in the cell sorter, all cells survived.
Computer simulations of the relevant photophysical and chemical reactions inside the irradiated cell were used to investigate the cause of this phenomenon. The results indicated that the absence of photoinactivation by DAO, after flash irradiations, was caused by the combined effects of (1) limited oxygen diffusion into the cell and (2) a reduced number of collisions between photosensitizer triplet and oxygen molecules during the irradiation due to saturation of the intracellular photosensitizer triplet concentration. The contributions of triplet-triplet annihilation and triplet quenching by ground state photosensitizer molecules were found to be minimal and not significant. These findings indicate that Type II photosensitizers are incapable of rapid selective photoinactivation in cell sorters.     

Molecular structure of ethynylbenzene from electron diffraction and ab initio molecular orbital calculations

The molecular structure and benzene ring distortions of ethynylbenzene have been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF/6-31G^* and 6-3G^** levels. Least-squares refinement of a model withC _2v, symmetry, with constraints from the MO calculations, yielded the following important bond distances and angles:r _g(C _i -C _o )=1.407±0.003 Å,r _g(C _o -C _m )=1.397±0.003 Å,r _g(C _m -C _p )=1.400±0.003 Å,r _g(Cr _i -CCH)=1.436 ±0.004 Å,r _g(C=C)=1.205±0.005 Å, C _o -C _i -C _o =119.8±0.4°. The deformation of the benzene ring of ethynylbenzene given by the MO calculations, including o-C_i-C_o=119.4°, is insensitive to the basis set used and agrees with that obtained by low-temperature X-ray crystallography for the phenylethynyl fragment, C₆H₅-CC-, in two different crystal environments. The partial substitution structure of ethynylbenzene from microwave spectroscopy is shown to be inaccurate in the ipso region of the benzene ring.