Direct Observation Method of Individual Single-Stranded DNA Molecules Using Fluorescent Replication Protein A

Direct observation studies of single molecules have revealed molecular behaviors usually hidden in the ensemble and time-averaging of bulk experiments. Direct single DNA molecule analysis of DNA metabolism reactions such as DNA replication, repair, and recombination is necessary to fully understand these essential processes. Intercalation of fluorescent dyes such as YOYO-1 and SYTOX Orange has been the standard method for observing single molecules of double-stranded DNA (dsDNA), but effective fluorescent dyes for observing single molecules of single-stranded DNA (ssDNA) have not been found. To facilitate direct single-molecule observations of DNA metabolism reactions, it is necessary to establish methods for discriminating ssDNA and dsDNA. To observe ssDNA directly, we prepared a fusion protein consisting of the 70 kDa DNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). This fusion protein had ssDNA-binding activity. In our experiments, dsDNA was stained by SYTOX Orange and ssDNA by RPA-YFP, and we succeeded in staining ssDNA and dsDNA by using RPA-YFP and SYTOX Orange simultaneously.     

A note on skew differential operators on commutative rings

Let A be a commutative integral domain that is a finitely generated algebra over a field k of characteristic 0 and let ø be a k-algebra automorphism of A of finite order m. In this note we study the ring D(A;ø of differential operators introduced by A.D. Bell. We prove that if A is a free module over the fixed sub-ring A ^ø, with a basis containing 1, then D(A;ø) is isomorphic to the matrix ring M_m(D(A ^ø). It follows from Grothendieck's Generic Flatness Theorem that for an arbitrary A there is an element c?Asuch that D(A[c^-1];ø)?M _m(D(A[c^-1]^ø)). As an application, we consider the structure of D(A;ø)when A is a polynomial or Laurent polynomial ring over k and ø is a diagonalizable linear automorphism.     

Conversion ratio to F-H center pairs from self-trapped excitons in alkali chloride crystals

Abstract

The time delayed double excitation spectroscopy has been utilized to determine the conversion ratio to F-H center pairs from self-trapped excitons(STE_L) at the lowest state (1s[sgrave]_g;a_1g). The final conversion ratios, η_F/(η_F+η_X), were 0.86, 0.49 and 0.20 for NaCl, KCl and RbCl at 14K, respectively. The conversion efficiency (η =η_F+η_X) from STE_L to F-H center pairs(η_F) and to unknown states(η_X) were 0.25, 0.90 and 0.76 for the hole excitation to π_g, while 0.03, 0.01 and 0.01 for the electron excitation to b_1u, b_2u or b_3u, in NaCl, KCl and RbCl, respectively.     

A CASCI-MRMP method based on Kohn—Sham orbitals

Kohn-Sham orbitals are used in the previously proposed CASCI-MRMP scheme (a multi-reference M?ller-Plesset (MRMP) method with a complete active space configuration interaction (CASCI) reference function). That is, the CASCI wave function was constructed using the Kohn-Sham orbitals and used as a reference function of the MRMP to incorporate the remaining dynamical correlation. The scheme was applied to the potential curves of the ground and low-lying excited states of N₂, the potential curve of the ground state of CO, the barrier height of the H₂CO → H₂ + CO reaction, the valence π-π? and Rydberg excited states of benzene, and the low-lying excited states of ozone. Good agreement between the theory, experiment, and some benchmark calculations was obtained. The various orbitals which are investigated here do not give very different results. Rather, the choice of active space makes a considerable difference, and in particular the perturbation calculation is proved to be very important.     

Selective Activation of Aromatic Aldehydes Promoted by Dispersion Interactions: Steric and Electronic Factors of a π-Pocket within Cage-Shaped Borates for Molecular Recognition

Selective bond formations are one of the most important reactions in organic synthesis. In the Lewis acid mediated electrophile reactions of carbonyls, the selective formation of a carbonyl–acid complex plays a critical role in determining selectivity, which is based on the difference in the coordinative interaction between the carbonyl and Lewis acid center. Although this strategy has attained progress in selective bond formations, the discrimination between similarly sized aromatic and aliphatic carbonyls that have no functional anchors to strongly interact with the metal center still remains a challenging issue. Herein, this work focuses on molecular recognition driven by dispersion interactions within some aromatic moieties. A Lewis acid catalyst with a π-space cavity, which is referred to as a π-pocket, as the recognition site for aromatic carbonyls is designed. Cage-shaped borates 1 B with various π-pockets demonstrated significant chemoselectivity for aromatic aldehydes 3 b – f over that of aliphatic 3 a in competitive hetero-Diels–Alder reactions. The effectiveness of our catalysts was also evidenced by intramolecular recognition of the aromatic carbonyl within a dicarbonyl substrate. Mechanistic and theoretical studies demonstrated that the selective activation of aromatic substrates was driven by the preorganization step with a larger dispersion interaction, rather than the rate-determining step of the C−C bond formation, and this was likely to contribute to the preferred activation of aromatic substrates over that of aliphatic ones.     

Magnetic Correlation Engineering in Spin-Sandwiched Layered Magnetic Frameworks

The insertion of “sandwiched spins” between magnetic layers could efficiently affect the interlayer magnetic correlations, but doing so increases the complexity in the interlayer spin alignment because of competition between the inserted spin-layer interaction J_NNI and the interlayer through-space interaction J_NNNI if the magnitude of J_NNI is of the same order as J_NNNI with reciprocal signs of the respective interactions. Herein, systematic tuning of the magnetic phase variations by J_NNI and J_NNNI in two kinds of metal-variable isostructural series of supramolecular pillared layer magnets [MCp*₂][{Ru₂^II,II(2,3,5,6-F₄CO₂)₄}₂(TCNQ)] ⋅ 2 DCE (M=Co, Fe, Cr; 2,3,5,6-F₄PhCO₂⁻=2,3,5,6-tetrafluorobenzoate; TCNQ=7,7,8,8-tetracyano-p-quinodimethane; DCE=1,2-dichloroethane) and their DCE-free series, in which [MCp*₂]⁺ (Cp*=η⁵-C₅Me₅) species with S=0, 1/2, and 3/2 for M=Co, Fe, Cr, respectively, are sandwiched between ferrimagnetic layers of [{Ru₂}₂(TCNQ)]⁻, is demonstrated. The results showed that the flexible magnetic natures of these magnets are changeable in dependence on J_NNI and J_NNNI, as well as on interlayer inserted spins M.     

Total Syntheses of Juglorescein and Juglocombins A and B

Total syntheses of juglorescein and juglocombins A and B are reported. The highly oxygenated 6/6/5/6/6‐fused pentacyclic ring system of these natural products was constructed through a bioinspired dimerization of 1,4‐naphthoquinone. Notably, five new stereogenic centers were constructed in a single step by the dimerization reaction. The epoxide intermediate obtained from the dimerization was successfully converted into juglocombins A and B through photoinduced reduction of the epoxide, dehydration, and conversion of the resultant quinone into a hydroquinone derivative. The same epoxide intermediate was also converted into a dicarboxylic acid, which was transformed into juglorescein through intramolecular lactonization, hydrolysis of the resulting lactone, and removal of the protecting groups. Furthermore, the relative and absolute configurations of juglorescein and juglocombins A and B were determined.     

Growth of high-quality ZnO single crystals by seeded CVT using the newly designed ampoule

The high-quality ZnO single crystals were grown by seeded chemical vapor transport (CVT) in a newly designed ampoule using carbon as a transport agent. The well-faceted crystal of about 5×5×5 mm³ can be grown reproducibly. Secondary ion mass spectroscopy (SIMS) analysis, X-ray rocking curve (XRC) and photoluminescence (PL) measurements demonstrate that the grown single crystal is of high purity and high crystallinity.     

Cameron-Martin formula for the σ-finite measure unifying Brownian penalisations

Quasi-invariance under translation is established for the σ-finite measure unifying Brownian penalisations, which has been introduced by Najnudel, Roynette and Yor [J. Najnudel, B. Roynette, M. Yor, A remarkable σ-finite measure on C(R₊,R) related to many Brownian penalisations, C. R. Math. Acad. Sci. Paris 345 (8) (2007) 459-466]. For this purpose, the theory of Wiener integrals for centered Bessel processes, due to Funaki, Hariya and Yor [T. Funaki, Y. Hariya, M. Yor, Wiener integrals for centered Bessel and related processes. II, ALEA Lat. Am. J. Probab. Math. Stat. 1 (2006) 225-240 (electronic)], plays a key role.