Effects of halogenated WNA derivatives on sequence dependency for expansion of recognition sequences in non-natural-type triplexes

Triplex-forming oligonucleotides (TFOs) are sequence-specific DNA-binding agents, but their target duplexes are limited to homopurine/homopyrimidine sequences because of interruption of the pyrimidines bases in the purine region. This problem has not been fully solved despite a wide variety of studies. Recently, we have developed a bicyclic system as a novel scaffold for nucleoside analogues (WNA, W-shaped nucleoside analogues) and determined two useful compounds, WNA-betaT (2) and WNA-betaC (5), for highly stable and selective triplex formation at a TA and a CG interrupting site, respectively. However, subsequent investigations have shown that the triplex formation using WNA is dependent on the neighboring bases of the TFOs. In this study, we have synthesized new WNA derivatives having halogenated recognition bases or benzene rings and evaluated the effects of the modifications on the triplex stability as well as selectivity. It has been found that the WNA-betaT analogues holding 5-halogenated pyrimidine bases (WNA-beta(Br)U (3) and WNA-beta(F)U (4)) exhibit high CG-selectivity. On the other hand, the WNA-betaT derivatives having the bromo-substituted benzene ring (mBr-WNA-betaT (10) and oBr-WNA-betaT (11)) have shown high selectivity to a TA interrupting site with high stability in the sequences to which the original WNA-betaT do not bind. Thus, sequence-dependency has been overcome by the sequence-dependent use of WNA-betaT, mBr-WNA-betaT, and oBr-WNA-betaT.     

Alkylthio unit as an alpha-pyrrole protecting group for use in dipyrromethane synthesis

The synthesis of porphyrin precursors requires the successive introduction of substituents at the pyrrole alpha- and alpha'-positions (2- and 5-, respectively). An alpha-pyrrole substituent that serves as a temporary masking agent and is not deactivating would greatly facilitate such syntheses, particularly for beta-(3,4)-unsubstituted pyrroles, but has heretofore not been available. A series of alpha-RS groups (R = Me, Et, n-decyl, Ph) have been investigated in this regard, including the determination of the kinetics of substitution at the pyrrolic 3-, 4-, and 5-positions and the application to dipyrromethane formation. The RS group was readily introduced into the pyrrole alpha-position by the reaction of 2-thiocyanatopyrrole (prepared from pyrrole, ammonium thiocyanate, and iodine) and the corresponding Grignard reagent RMgBr. Each 2-alkylthio group activated the pyrrole ring toward deuteration at the 3- or 5- (vs 4-) position. The dipyrromethane synthesis was carried out using a 2:1 ratio of 2-(RS)pyrrole/benzaldehyde with a catalytic amount of InCl3 at room temperature in the absence of any solvent. The alpha-RS group was removed by hydrodesulfurization using Raney nickel or nickel complexes. This stoichiometric synthesis using the alpha-RS-protected pyrrole is in contrast to the traditional synthesis that employs an aldehyde and 25-100 mol equiv of pyrrole. Six meso-substituted dipyrromethanes were prepared by the reaction of 2-(n-decylthio)pyrrole/aldehyde/InCl3 (2.2:1:0.2 ratio) followed by hydrodesulfurization. Other reactions of the 1,9-bis(RS)dipyrromethane include oxidation to give (i) the 1,9-bis(RS)dipyrrin or (ii) the 1,9-bis(RSO2)dipyrromethane, which underwent subsequent complexation with dibutyltin dichloride. In summary, under mild reaction conditions, the 2-alkylthio group is readily introduced to the pyrrole nucleus, directs electrophilic substitution to the 5-position, and is readily removed as required for elaboration of porphyrinic precursors.     

Triradical cation of p-phenylenediamine having two nitroxide radical groups: spin alignment mediated by delocalized spin

The cationic state of a p-phenylenediamine (PDA) molecule having two nitroxide radical groups was prepared and characterized using electrochemical, electron spin resonance (ESR) spectroscopic, and absorption spectroscopic methods. The delocalized intervalence state of the p-phenylendiamine (PDA) moiety was detected in the cationic state. From the pulsed ESR measurements, it was confirmed that the delocalized spin induces parallel spin alignment between the localized two nitroxide groups which are magnetically weakly coupled in the neutral state. It was found that the resulting high-spin alignment does not seriously affect the delocalized intervalence state of the PDA radical cation.     

Scaling and universality of roughening in thermal oxidation of Si(001)

By analyzing atomic force microscopy images, we derive a continuum equation that quantitatively explains the roughening at the Si(001)-SiO2 interface during thermal oxidation at the temperature at 1200 degrees C in an Ar atmosphere containing a small fraction of O2. We also show that there is a phase transition in the universality class from a disordered to step-terrace structure at the interface at oxidation temperatures between 1150 and 1380 degrees C with the miscut angle of the substrate as the scaling parameter.     

Palladium-catalyzed asymmetric silaboration of allenes

An enantioselective silaboration of allenes was achieved using an achiral silylborane in the presence of a palladium catalyst bearing a chiral monodentate phosphine ligand. (R)-2-Bis(3,5-dimethylphenyl)phosphino-1,1'-binaphthyl gave the highest enantioselectivities in the addition of (diphenylmethylsilyl)pinacolborane to the internal C=C bond of terminal allenes at 0 degrees C, giving the corresponding beta-borylallylsilanes in high yields with high enantiomeric excesses. The enantioselectivity depended on the bulkiness of substituents of allenes: the enantiomeric excesses were found to be 91-93% ee (R = tert- and sec-alkyl), 88-90% ee (R = aryl), and 80-82% ee (R = prim-alkyl and Me) at 0 degrees C. Perfect chirality transfer was observed in the intramolecular cyclization reactions of the functionalized allylsilanes, affording highly enantioenriched cyclic alkenylboranes, which underwent Suzuki-Miyaura coupling with aryl halides.     

Conformational analysis of chiral helical perfluoroalkyl chains by VCD

Vibrational circular dichroism (VCD) technique successfully revealed the absolute configuration of the biased helix of perfluoroalkyl chains in solution with the aid of theoretical calculations, which was supported by an X-ray crystallographic study.     

Highly enantioselective synthesis of atropisomeric anilide derivatives through catalytic asymmetric N-arylation: conformational analysis and application to asymmetric enolate chemistry

In the presence of (R)-DTBM-SEGPHOS-Pd(OAc)(2) catalyst, N-arylation (aromatic amination) of various o-tert-butylanilides with p-iodonitrobenzene proceeds with high enantioselectivity (88-96% ee) to give atropisomeric N-(p-nitrophenyl)anilides having an N-C chiral axis in good yields. Atropisomeric anilide products highly prefer to exist as the E-rotamer which has trans-disposed o-tert-butylphenyl group and carbonyl oxygen. The application of the present catalytic enantioselective N-arylation to an intramolecular version gives atropisomeric lactam derivatives with high optical purity (92-98% ee). The reaction of the lithium enolate prepared from the atropisomeric anilide and lactam products with various alkyl halides gives alpha-alkylated products with high diastereoselectivity (diastereomer ratio = 13:1 to 46:1).     

High-pressure studies of optical dephasing in polymer glasses

The effect of high pressure on the optical dephasing of chromophores in organic polymers at low temperature is evaluated within the stochastic sudden jump two-level-system (TLS) model. The approximations within the "standard" TLS model cannot account for the observed pressure dependence of the pure dephasing rate without ad hoc assumptions about changes in the TLS density of states. However, the photon echo model of Geva and Skinner for disordered systems can be used to model pressure-dependent optical dephasing results for a variety of doped polymer systems without assuming changes in the TLS density of states. The relative importance of pressure-induced changes in TLS density, chromophore-TLS coupling, and TLS-phonon coupling is evaluated by fitting experimental high-pressure photon echo results to the TLS model.     

Characterization of linear and cyclic polylactic acids and their solvolysis products by electrospray ionization mass spectrometry

Linear and cyclic polylactic acids (PLAs) were characterized using electrospray ionization mass spectrometry (ESI-MS) as part of our ongoing investigation of the hydrolysis mechanism of biodegradable polymers. The condensation oligomers of linear polylactic acid (LPLA) were synthesized by thermal dehydration of L-lactic acid. The trimer and tetramer base polymers of cyclic polylactic acid (CPLA) were obtained by cyclization reactions of lactic acid trimers and tetramers, respectively. In the ESI-MS/MS measurement, LPLA yielded three types of product ion series, while CPLA yielded only one type, from which the repeated units of CPLA were removed. The MS/MS spectrum of the NH4+ adduct ion for both cyclic and linear PLA showed loss of one ammonia molecule. The postsource decay (PSD) spectrum of CPLA by matrix-assisted laser desorption ionization (MALDI) mass spectrometry was similar to the ESI-MS/MS spectrum, while that of LPLA was different. In addition, the degradation of cyclic and linear PLAs by solvolysis was investigated. Solvolysis with anhydrous MeOH was quite feasible, but did not readily occur in the presence of even a small amount of water in the MeOH solvent.     

Synthesis of tris(tetrathiafulvaleno)dodecadehydro- [18]annulenes and their self-assembly

[reaction: see text] Synthesis of electroactive tris(tetrathiafulvaleno)dodecadehydro[18]annulenes with ester substituents has been carried out with palladium-mediated cyclotrimerization of 4,5-diethynyl-TTFs. The TTF[18]annulenes produce stacked dimmers in solution and exhibit solvatochromism and thermochromism. The TTF[18]annulene-hexabutyl ester forms a molecular wire from an aqueous THF solution with cooperative S-S and pi-pi stacking interactions.