New nucleotide pairs for stable DNA triplexes stabilized by stacking interaction

New nucleotide pairs applicable to formation of DNA triplexes were developed. We designed oligonucleotides incorporating 5-aryl deoxycytidine derivatives (dC5Ars) and cyclic deoxycytidine derivatives, dCPPP and dCPPI, having an expanded aromatic area, as the second strand. As pairing partners, two types of abasic residues (C3: propylene linker, phi: abasic base) were chosen. It was concluded that, when the 5-aryl-modified cytosine bases paired with the abasic sites in TFOs in a space-fitting manner, the stability of the resulting triplexes significantly increased. The recognition of C3 toward dC5Ars was selective because of the stacking interactions between their aromatic part and the nucleobases flanking the abasic site. These results indicate the potential utility of new nucleotide triplets for DNA triplex formation, which might expand the variety of structures and sequences and might be useful for biorelated fields such as DNA nanotechnologies.     

Evidence for the cation-pi interaction between Cu2+ and tryptophan

The cation-pi interaction, a noncovalent interaction of electrostatic nature between a cation and an electron-rich pi system, is increasingly recognized as an important force that influences the structures and functions of molecules including proteins. Unlike other metal cations, the transition metal cation Cu2+ is not regarded to take part in a cation-pi interaction because Cu2+ tends to oxidize the pi electron system, in particular that of Trp, and to introduce covalency in the metal-pi electron interaction. This paper reports the first spectral evidence for the cation-pi interaction between Cu2+ and Trp. The Cu2+ ion bound to the amino N-terminal Cu2+/Ni2+ binding motif composed of three amino acid residues interacts with the indole ring of the fourth Trp residue in a noncovalent manner. The Cu2+-Trp interaction produces a distinct negative band at 223 nm in circular dichroism (CD), which disappears upon mutation or depletion of the Trp residue or upon replacement of the Cu2+ ion by Ni2+. In UV absorption, a pair of negative/positive intensity changes is generated at 222/231 nm by the Cu2+-Trp interaction, being consistent with the previous observations on the indole ring interacting with K+ or a cationic His imidazole ring. The negative CD band around 223 nm is characteristic of the Cu2+-Trp pair and may be useful as a marker of the Cu2+-Trp cation-pi interaction. Coordination of negatively charged ligands to Cu2+ is suggested to be important for the cation to be involved in a cation-pi interaction.     

Chiral ammonium betaines: a bifunctional organic base catalyst for asymmetric Mannich-type reaction of alpha-nitrocarboxylates

A chiral ammonium betaine, an intramolecular ion-pairing quaternary ammonium aryloxide 3, has been designed and its vast potential as an enantioselective organic base catalyst has been successfully demonstrated in the highly enantioselective direct Mannich-type reaction of alpha-substituted alpha-nitrocarboxylates 2 with various N-Boc imines 1. The present study provides a conceptually new approach toward the design of bifunctional, chiral quaternary ammonium salts and their utilizations as a homogeneous organic molecular catalyst.     

Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide

Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.     

TMG-chitotriomycin, an enzyme inhibitor specific for insect and fungal beta-N-acetylglucosaminidases, produced by actinomycete Streptomyces anulatus NBRC 13369

A novel beta-N-acetylglucosaminidase (GlcNAcase) inhibitor named TMG-chitotriomycin (1) was isolated from the culture filtrate of Streptomyces anulatus NBRC13369. The strain produced 1 only when colloidal chitin was used as the sole carbon source in the production medium. The structure of 1 was determined by spectral and constitutive sugar analyses of the corresponding alditol derivatives to be an equilibrated mixture of alpha-d-N,N,N-triMeGlcNH2-(1,4)-beta-d-GlcNAc-(1,4)-beta-d-GlcNAc-(1,4)-d-GlcNAc and its C-2 epimer of the reducing end residue. TMG-chitotriomycin (1) showed potent and selective inhibition of insect and fungal GlcNAcases with no inhibition of mammalian and plant GlcNAcases. In contrast, the known GlcNAcase inhibitor nagstatin potently inhibited all GlcNAcases. It should be emphasized that synthesized d-N,N,N-triMeGlcNH2, which is the component sugar of 1, showed no inhibition of the insect Spodoptera litura GlcNAcase. These results suggest that the (GlcNAc)3 unit positioned at the reducing end of 1 is essential for its enzyme inhibitory activity. The unique inhibitory spectrum of 1 will be useful to study chitinolytic systems and to develop selective fungicides or pesticides.     

Syntheses, structures, and coordination chemistry of phosphole-containing hybrid calixphyrins: promising macrocyclic P,N2,X-mixed donor ligands for designing reactive transition-metal complexes

The syntheses, structures, and coordination chemistry of phosphole-containing hybrid calixphyrins (P,N2,X-hybrid calixphyrins) and the catalytic activities of their transition-metal complexes are reported. The 5,10-porphodimethene type 14pi-P,(NH)2,X- and 16pi-P,N2,X-hybrid calixphyrins (X = O, S, NH) are prepared via acid-promoted dehydrative condensation between a sigma4-phosphatripyrrane and the corresponding 2,5-bis[hydroxy(phenyl)methyl]heteroles followed by DDQ oxidation. Both spectroscopic and crystallographic data of the hybrid calixphyrins have revealed that the conformation and size of the macrocyclic platforms as well as the oxidation state of the -conjugated pyrrole-heterole-pyrrole (N-X-N) units vary considerably depending on the combination of heteroles. The sigma3-P,(NH)2,S- and sigma3-P,N2,S-hybrids react with Pd(OAc)2 and Pd(dba)2, respectively, to afford the same Pd(II)-P,N2,S-hybrid complex, in which the calixphyrin platform is regarded as a dianionic ligand. In the complexation with [RhCl(CO)2]2 in dichloromethane, the sigma3-P,N2,S-hybrid behaves as a neutral ligand to afford an ionic Rh(I)-P,N2,S-hybrid complex, whereas the sigma3-P,N2,NH-hybrid behaves as an anionic ligand to produce Rh(III)-P,N3-hybrid complexes. In the latter reaction, it is likely that a neutral Rh(I)-P,N3-hybrid complex, generated as a highly nucleophilic intermediate, undergoes C-Cl bond activation of the solvent. The complexation of AuCl(SMe2) with the sigma3-P,N2,X-hybrids (X = S, NH) leads to the formation of the corresponding Au(I)-monophosphine complexes. The spectral data and crystal structures of these metal complexes exhibit the hemilabile nature of the phosphole-containing hybrid calixphyrin platforms derived from the flexible phosphole unit and the redox active N-X-N units. The hybrid calixphyrin-palladium and -rhodium complexes catalyze the Heck reaction and hydrosilylations, respectively, implying that the metal center in the core is capable of activating the substrates under appropriate reaction conditions. The present results demonstrate the potential utility of the phosphole-containing hybrid calixphyrins as a new class of macrocyclic P,N2,X-mixed donor ligands for designing highly reactive transition-metal complexes.     

Alkaline extraction in combination with microwave-assisted extraction followed by solid-phase extraction treatment for polycyclic aromatic hydrocarbons in a sediment sample

Microwave-assisted extraction using 1 M KOH/methanol (alkaline-MAE) in combination with solid-phase extraction treatment was developed and applied to polycyclic aromatic hydrocarbons (PAHs) in a sediment sample. Although various conditions were examined (100 or 150 °C for 10 or 30 min), comparable concentrations of PAHs to those obtained by conventional extraction with 1 M KOH/methanol at 70 °C for 4 h were obtained, even at 100 °C for 10 min. The concentrations obtained by using MeOH at 150 °C for 30 min without KOH were lower (by 1.3-37%) than those obtained by alkaline-MAE at 150 °C for 30 min. Since the developed technique can introduce higher concentration of benzo[ghi]perylene relative to those using pressurized liquid extraction (toluene, 150 °C, 15 MPa, 10 min, two cycles), the developed alkaline-MAE is a effective technique.     

Polymer-like polyphenols of black tea and their lipase and amylase inhibitory activities

Lipase and amylase inhibitory activities of black tea were examined. After solvent partitioning of a black tea extract with the ethyl acetate and n-butanol, the two soluble fractions showed comparable inhibitory activities. Activity in the ethyl acetate fraction was mainly attributable to polyphenols with low-molecular weights, such as theaflavin gallates. On the other hand, the active substance in the n-butanol layer was ascertained to be a polymer-like substance. 1H- and 13C-NMR spectra showed signals arising from the flavan A-ring and galloyl groups, although signals due to flavan B-rings were not detected, suggesting that the polymer-like substances were generated by oxidative condensation of flavan B-rings, a result which was previously deduced from our results of in vitro catechin oxidation experiments. Enzymatic oxidation of epicatechin 3-O-gallate produced a similar polymer-like substance and suggested that condensation between a B-ring and galloyl groups was involved in the polymerization reaction.