Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis

Capillary electrophoretic separation of 60 mer single-stranded DNA (ssDNA) and a single-base-substituted ssDNA was demonstrated using a size- and composition-controlled poly(ethylene glycol)-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as an affinity ligand. Under appropriate conditions, PEG-b-ODN and ssDNA with a complementary sequence formed a reversible complex via hybridization during the electrophoresis, while the copolymer did not interact with the single-base-substituted ssDNA. The copolymer's PEG length determined the electrophoretic mobility of the ssDNA; upon formation of the complex, the electrically neutral PEG added hydrodynamic friction to ssDNA. Simultaneously using two types of PEG-b-ODN copolymers whose PEG segments were of different lengths, we achieved the complete separation of the 60 mer ssDNA, its single-base-substituted ssDNA, and impurities. This method was sensitive enough to quantify a slight amount (approximately 1%) of the single-base-substituted ssDNA. The present results suggest that our approach is applicable to quantitative detection of minor genotypes.     

Total synthesis of (-)-kainic acid via intramolecular Michael addition: a second-generation route

A total synthesis of (-)-kainic acid starting from the commercially available 2-azetidinone is described. The key delta-lactone intermediate was concisely prepared from the commercially available azetidinone through the Reformatsky-type reaction and an introduction of a glycine moiety. The construction of the functionalized pyrrolidine ring was executed by a one-pot sequential elimination-Michael addition protocol of a beta-amino-delta-lactone intermediate with high diastereoselectivity.     

Synthesis of maremycins A and D1 via cycloaddition of a nitrone with (E)-3-ethylidene-1-methylindolin-2-one

A concise synthesis of maremycins A and D1 has been accomplished via cycloaddition of a chiral cyclic nitrone with ( E)-3-ethylidene-1-methylindolin-2-one as a key step. This synthesis clarifies the stereochemistry of the maremycins and is suitable for large-scale synthesis for biological screening.     

A mild inter- and intramolecular amination of aryl halides with a combination of CuI and CsOAc

A unique combination of CuI and CsOAc was found to catalyze aryl amination under mild conditions. The reaction takes place at room temperature or at 90 °C with broad functional group compatibility. The intramolecular reaction was able to form five-, six-, and seven-membered rings with various protecting groups on the nitrogen atom. The scope of the intermolecular amination, as well as its applications to unsymmetrical N,N′-dialkylated phenylenediamines, was investigated.     

Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides

Molecular dynamics (MD) simulation using the reference potential spatial warping algorithm (REPSWA) is a promising method for computing the conformational equilibrium of a system with a rugged energy surface. Its effectiveness has previously been demonstrated using only a simplified model system of a hydrocarbon chain omitting nonbonded interaction terms from the potential energy function. To evaluate the applicability of REPSWA MD simulation to more realistic problems, we applied it to small peptide systems in an aqueous environment. Difficulties were encountered, however, forcing us to devise several modifications. We investigated their effectiveness in comparison to conventional constant-temperature and multicanonical MD simulations. We found that the sampling efficiency of the modified REPSWA MD after a careful optimization of its parameters was better than that of the constant-temperature MD and comparable to that of the multicanonical MD in several cases.     

Absolute configurations of endoperoxides determined by vibrational circular dichroism (VCD)

Diastereomeric mixture on the peroxide portion of an endoperoxide acetylmajapolene A (1) was efficiently separated by HPLC on a chiral column, submitting to vibrational circular dichroism (VCD) investigation. The ab initio theoretical VCD and IR calculations of 1a and 1b were performed by density functional theory (DFT) using the B3PW91/6-31G(d,p) level of theory. Focusing on an isolated characteristic peroxide vibrational band, absolute configurations of 1a and 1b were unambiguously determined as (1R,4R,7S,10S) and (1S,4S,7S,10S), respectively. This is the first VCD application to endoperoxides which exist abundantly in nature.     

Bond fluctuation of S/Se anchoring observed in single-molecule conductance measurements using the point contact method with scanning tunneling microscopy

Conductance was measured for the single molecules with S/Se anchoring on a Au surface using the point contact method with scanning tunneling microscopy that enables us to selectively perform a repeated analysis of a chosen target molecule. Apparent conductance changes observed in sequential measurements suggest the existence of bond fluctuation among the adsorption sites.     

Terthiophene radical cations end-capped by bicyclo[2.2.2]octene units: formation of bent pi-dimers mutually attracted at the central position

A terthiophene fused with bicyclo[2.2.2]octene units only at both ends was newly synthesized. Since there is no steric hindrance at the central position, this terthiophene has a possibility to interact only at the central position. One-electron oxidation of this terthiophene afforded a highly stable radical-cation salt as deep blue crystals. The result of X-ray crystal structural analysis demonstrated a characteristically bent pi-dimereric structure, which is formed by mutual attraction of single radical-cation species at the central position to minimize the steric repulsion. Remarkably short intermolecular distances between the central thiophene rings of each unit of the dimeric pair, that is, 2.976(10) A for Cbeta-Cbeta, 3.091(10) A for Calpha-Calpha, and 3.779(3) A for S-S, are good indication of the existence of attracting interaction, which was confirmed by theoretical calculations. This interaction was experimentally demonstrated by the reversible formation of the pi-dimer in CH2Cl2 solution using ESR and UV-vis-NIR spectroscopy. The crystal of the pi-dimer is in its singlet state and ESR silent in the solid state at 300 K, but the signal of a triplet state of the pi-dimer was observed by heating the solid at 400 K. This indicates that this pi-dimer has a quite small triplet-singlet enegy gap and the triplet state is thermally accessible.     

Experimental and theoretical evaluation of the charge distribution over the ruthenium and dioxolene framework of [Ru(OAc)(dioxolene)(terpy)] (terpy = 2,2':6',2' '-terpyridine) depending on the substituents

A series of ruthenium complexes [Ru(OAc)(dioxolene)(terpy)] having various substituents on the dioxolene ligand (dioxolene = 3,5-t-Bu2C6H2O2 (1), 4-t-BuC6H3O2 (2), 4-ClC6H3O2 (3), 3,5-Cl2C6H2O2 (4), Cl4C6O2 (5); terpy = 2,2':6'2' '-terpyridine) were prepared. EPR spectra of these complexes in glassy frozen solutions (CH2Cl2:MeOH = 95:5, v/v) at 20 K showed anisotropic signals with g tensor components 2.242 > g1 > 2.104, 2.097 > g2 > 2.042, and 1.951 > g3 > 1.846. An anisotropic value, Deltag = g1 - g3, and an isotropic g value, g = [(g1(2) + g2(2) + g3(2))/3]1/2, increase in the order 1 < 2 < 3 < 4 < 5. The resonance between the Ru(II)(sq) (sq = semiquinone) and Ru(III)(cat) (cat = catecholato) frameworks shifts to the latter with an increase of the number of electron-withdrawing substituents on the dioxolene ligand. DFT calculations of 1, 2, 3, and 5 also support the increase of the Ru spin density (Ru(III) character) with an increase of the number of Cl atoms on the dioxolene ligand. The singly occupied molecular orbitals (SOMOs) of 1 and 5 are very similar to each other and stretch out the Ru-dioxolene frameworks, whereas the lowest unoccupied molecular orbital (LUMO) of 5 is localized on Ru and two oxygen atoms of dioxolene in comparison with that of 1. Electron-withdrawing groups decrease the energy levels of both the SOMO and LUMO. In other words, an increase in the number of Cl atoms in the dioxolene ligand results in an increase of the positive charge on Ru. Successive shifts in the electronic structure between the Ru(II)(sq) and Ru(III)(cat) frameworks caused by the variation of the substituents are compatible with the experimental data.     

4-(Pyrrolidinyl)methoxybenzoic acid derivatives as a potent, orally active VLA-4 antagonist

A novel series of benzoic acid derivatives as VLA-4 antagonists were synthesized. Optimization, focusing on activity and lipophilicity needed for cell permeability, resulted in the identification of 15b and 15e with good activity (IC50 = 1.6 nM each) and moderate lipophilicity (Log D = 2.0, 1.8). Furthermore, 15e demonstrated efficacy in murine asthma model by an oral dose of 30 mg/kg.