An efficient unnatural base pair for PCR amplification

Expansion of the genetic alphabet by an unnatural base pair system provides a powerful tool for modern biotechnology. As an alternative to previous unnatural base pairs, we have developed a new pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitropyrrole (Pn), which functions in DNA amplification. Pn more selectively pairs with Ds in replication than another previously reported pairing partner, pyrrole-2-carbaldehyde (Pa). The nitro group of Pn efficiently prevented the mispairing with A. High efficiency and selectivity of the Ds-Pn pair in PCR amplification were achieved by using a substrate mixture of the gamma-amidotriphosphate of Ds and the usual triphosphates of Pn and the natural bases, with Vent DNA polymerase as a 3' to 5' exonuclease-proficient polymerase. After 20 cycles of PCR, the total mutation rate of the Ds-Pn site in an amplified DNA fragment was approximately 1%. PCR amplification of DNA fragments containing the unnatural Ds-Pn pair would be useful for expanded genetic systems in DNA-based biotechnology.     

Mechanistic study of a Pd/C-catalyzed reduction of aryl sulfonates using the Mg-MeOH-NH(4)OAc system

A method for the deoxygenation of phenolic hydroxy groups via aryl triflates or mesylates has been established by using a combination of Pd/C-Mg-MeOH. The addition of NH(4)OAc to the system markedly accelerated the reaction rate and expanded the scope of the reaction. Mechanistic studies suggested that a single-electron transfer process from the Pd(0) center to the benzene ring is involved in the reduction of aryl sulfonates and that NH(4)OAc works as a solubilization reagent of the Mg salt and as an accelerator of the electron transfer, thus enhancing the reaction process. Our method was also applicable to the regioselective deuteration of benzene derivatives with CH(3)OD as the solvent and deuterium source: the original hydroxy group could be efficiently replaced with a deuterium atom.     

Theoretical study of the double Renner effect for A2Pi MgNC/MgCN: higher excited rovibrational states

The authors report here the implementation of a newly developed, highly efficient matrix diagonalization routine in the DR program [T. E. Odaka et al., J. Mol. Struct. 795, 14 (2006)]. The DR program solves the rovibronic Schrodinger equation for a triatomic molecule with a double Renner effect, i.e., with two accessible linear arrangements of the nuclei at which the electronic energy is doubly degenerate. With the new routines, the authors can extend the DR calculations of rovibronic energies for A 2Pi MgNC/MgCN by considering a much larger set of rovibronic states, in particular, states at higher J values, than the authors were able to access previously.     

Ab initio molecular orbital study of ground and low-lying electronic states of CoCN

The ground and low-lying excited states of CoCN have been studied by ab initio multireference single and double excitation configuration interaction (MR-SDCI) calculations with Davidson's correction Q and Cowan-Griffin's relativistic corrections. The electronic ground state of CoCN is (3)Phi(i) and the equilibrium geometry is linear with bond lengths of r(e)(Co-C)=1.8540 A and r(e)(C-N)=1.1677 A, substantially different from the experimentally derived values of r(0)(Co-C)=1.8827(7) A and r(0)(C-N)=1.1313(10) A. The first excited state is (3)Delta(i), separated from the ground state by 727 cm(-1). Larger dynamical electron correlation energy for the low-spin (3)Phi state than for the high-spin (5)Phi state makes the (3)Phi state to be the ground state, which is discussed in terms of the differences in natural orbitals. A new spin-orbit interaction scheme between the X (3)Phi(i) and 1 (3)Delta(i) states is proposed.     

Colloidal crystals of core-shell type spheres with poly(styrene) core and poly(ethylene oxide) shell

Elastic modulus and crystal growth kinetics have been studied for colloidal crystals of core–shell type colloidal spheres (diameter = 160–200 nm) in aqueous suspension. Crystallization properties of three kinds of spheres, which have poly(styrene) core and poly(ethylene oxide) shell with different oxyethylene chain length (n = 50, 80 and 150), were examined by reflection spectroscopy. The suspensions were deionized exhaustively for more than 1 year using mixed bed of ion-exchange resins. The rigidities of the crystals range from 0.11 to 120 Pa and from 0.56 to 76 Pa for the spheres of n = 50 and 80, respectively, and increase sharply as the sphere volume fraction increase. The g factor, parameter for crystal stability, range from 0.029 to 0.13 and from 0.040 to 0.11 for the spheres of n = 50 and 80, respectively. These g values indicate the formation of stable crystals, and the values were decreased as the sphere volume fraction increased. Two components of crystal growth rate coefficients, fast and slow, were observed in the order from 10⁻³ to 10¹ s⁻¹. This is due to the secondary process in the colloidal crystallization mechanism, corresponding to reorientation from metastable crystals formed in the primary process and/or Ostwald-ripening process. There are no distinct differences in the structural, kinetic and elastic properties among the colloidal crystals of the different core–shell size spheres, nor difference between those of core–shell spheres and silica or poly(styrene) spheres. The results are very reasonably interpreted by the fact that colloidal crystals are formed in a closed container owing to long-range repulsive forces and the Brownian movement of colloidal spheres surrounded by extended electrical double layers, and their formation is not influenced by the rigidity and internal structure of the spheres.     

Rheological properties of deionized Chinese ink

Rheological properties for Chinese ink in exhaustively deionized aqueous media were carefully examined. In the steady shear measurement, the shear viscosities of the ink could be well explained by considering the “effective” volume fraction of the particles in the ink including the electrical double layers and by using Einstein's equation for dilute suspension viscosity, when the particle volume fraction was substantially low. In the case that the volume fraction was higher, the shear viscosities showed extremely higher than those from Einstein's prediction, though the ink remained a Newtonian liquid. In the stress-strain measurement, the shear moduli were observed at strain smaller than 0.2. The “weak” aggregation among the particles in the ink under no shear or low shear rates was supported. It should be noted that the glue in the suspension plays an important role for the good liquidity of the ink and for the “weak” bridges among the particles resulting its good dispersion stability.     

Quenching treatment for improvement of nonlinear optical response time in high-χ CuCl-doped glasses

Quenching treatments were performed on CuCl microcrystallite-doped glasses prepared by a melting method. Radiative decay time measurement and χ⁽³⁾ measurement for the quenched glasses were performed using ps and ns laser. The glasses showed that the radiative decay time were shortened by one order of magnitude without a decrease of third-order nonlinear susceptibility χ⁽³⁾ after the quenching treatment from above 300°C. The distorted structure of CuCl microcrystallites quenched from high temperature was considered to be most effective for the shortening of the lifetime of Z₃ exciton.     

Synthesis and structure of 8-hydroxy-6-methoxy-3,7-dimethylisochromane and its analogues

The title compound 1 was obtained by the reaction of alcohol 18 and triethyl orthoformate catalyzed by aluminum chloride followed by catalytic hydrogenation in good yield. Similarly, compounds 1 and 3 were obtained by intramolecular cyclization of MOM ether 19 with titanium(IV) chloride in moderate yields and isochromanes 1, 3, 26 and 27 by intramolecular cyclization of ether 20 with titanium(IV) chloride in high yields. The structures of compounds 1-3 were elucidated by analysis of spectroscopic data and chemical reactions. The mechanisms on the formation of 1 and 3 are discussed.     

Zinc chelation and photofluorochromic behavior of spironaphthoxazine intercalated into hydrophobically modified montmorillonite

Spironaphthoxazine (SNO) and Zn2+ were intercalated into montmorillonite interlayers hydrophobically modified by the alkyltrimethylammonium cation during UV light irradiation. The fluorescence spectra of the montmorillonite composites were observed to vary with an increase in the UV and visible light irradiation times. These composites exhibited two types of fluorescence emissions: F1, which originates from a new species, Xs, which is different from SNO (ring-closed form) and merocyanine (MC; ring-open form), and F2, which originates from the MC-Zn complex. With increasing UV light irradiation time, the F1 intensities decreased, whereas the F2 intensities increased. Xs, which is an intermediate species between SNO and MC, was transformed into MC and then coordinated with Zn2+ (i.e., MC-Zn complex) during the UV light irradiation. The reaction rate of the formation of the MC-Zn complex decreased for the hydrophobically modified montmorillonite due to a longer alkyl chain. The retrieval changes in the F1 and F2 intensities were observed with an increasing visible light irradiation time, implying the dissociation of the MC-Zn complex into Xs and Zn2+. The dissociation especially occurred for the hydrophobically modified montmorillonite with a longer alkyl chain. The formation and disappearance of Xs and the MC-Zn complex obeyed first-order kinetics, and therefore the interconversion between Xs and MC could be regarded as the rate-determining step of the whole reaction during the UV and visible light irradiations. The photoinduced reactions of the SNO species and Zn2+ were profoundly affected by the physicochemical environment provided by the clay interlayers. It is concluded that the present photoreactions can be controlled not only by the amounts of the intercalated SNO species and Zn2+, but also by the hydrophobic environment created by the surfactant molecules.