Development of the excimer probe responsible for DNA target bearing the silylated pyrenes at base moiety.

For the development of the excimer probe responsible for DNA target, the deoxyuridine phosphoramidite derivative bearing the silylated pyrene attached at the C-5 position was prepared and incorporated into oligonucleotides. The modified oligonucleotides showed the excimer emission in the absence of the target DNA, on the other hands, the excimer emission was quenched in the presence of the target DNA. For the utilization of the fluorescence behavior, the novel molecular beacon probe containing the silylated pyrene-modified nucleoside at the stem region was designed and the fluorescence property of the probe found to show the responsibility for DNA target.

Novel method of the synthesis and hybridization properties of an oligonucleotide containing non-ionic diisopropylsilyl internucleotide linkage.

Efficient synthesis of a dithymidine dinucleotide analog bearing a diisopropylsilyl linkage instead of a phosphodiester linkage is described with respect to its incorporation into oligonucleotides. The diisopropylsilyl linkage was introduced into the oligonucleotide by preparation of the phosphoramidite derivative of a dithymidine dimer unit. The diisopropylsilyl-modified oligonucleotide exhibited hybridization behavior with both single strand and duplex DNA.

Stabilizing effect of propionic acid derivative of anthraquinone--polyamine conjugate incorporated into α-β chimeric oligonucleotides on the alternate-stranded triple helix.

Two types of anthraquinone conjugates were synthesized as non-nucleosidic oligonucleotide components. These include an anthraquinone derivative conjugated with 2,2-bis(hydroxymethyl)propionic acid and an anthraquinone--polyamine derivative conjugated with 2,2-bis(hydroxymethyl)propionic acid. The conjugates were successfully incorporated into the "linking-region" of the α-β chimeric oligonucleotides via phosphoramidite method as non-nucleosidic backbone units.

Cholesterol biosynthesis pathway intermediates and inhibitors regulate glucose-stimulated insulin secretion and secretory granule formation in pancreatic beta-cells.

Cholesterol is reportedly abundant in the endocrine secretory granule (SG) membrane. In this study, we examined the involvement of cholesterol biosynthesis intermediates and inhibitors in insulin secretion and SG formation mechanisms. There are two routes for the supply of cholesterol to the cells: one via de novo biosynthesis and the other via low-density lipoprotein receptor-mediated endocytosis.

Investigation of the mechanism of the fluorescent emission of the silylated pyrene modified DNA.

Modified DNA containing silylated pyrene derivative at the 5'-terminus showed the obvious discrimination ability of the duplex formation, that the modified DNA showed the strong fluorescence emission in the presence of the complementary DNA, in spite of the very weak emission in the absence of the complementary DNA. The intensity of the fluorescence emission of the double strand found to increase about 10 times compared with that of the single strand. In this paper, we tried to disclose the detailed mechanism of such a discrimination ability of the silylated pyrene-modified DNA.

Synthesis and properties of oligonucleotides containing silylated pyrene derivatives.

Preparation and properties of the novel fluorescently labelled oligonucleotides, containing the silylated pyrene derivatives are reported. The silylated pyrene derivatives were introduced into both 5'-terminus and C-5 position of the deoxyuridine derivatives. The fluorescent spectra indicated the possibility of the discrimination of the duplex formation by the simple denaturation.

Spermine moiety attached to the C-5 position of deoxyuridine enhances the duplex stability of the phosphorothioate DNA/complementary DNA and shows the susceptibility of the substrate to RNase H.

Novel phosphorothioate-modified oligodeoxynucleotides (S-ODNs) containing a deoxyuridine derivative bearing a spermine moiety at the C-5 position were synthesized. The study of the thermal stability and the thermodynamic stability showed that the modified S-ODNs have been able to form the stable duplexes with the complementary DNA. It was also found that the duplex composed of the modified S-ODN and its complementary RNA strand is the substrate for Escherichia coli RNase H, and the cleavage of the RNA strand by the enzyme was almost similar as in the case of the unmodified one.

Synthesis, duplex-forming ability and fluorescent property of OligoDNA bearing silylated fluorophore.

Novel pyrene derivative conjugated with dimethylsilyl moiety was prepared from bromopyrene. The compound was successfully converted to the corresponding phosphoramidite derivative and incorporated into oligoDNA. In uv-melting study, the resulted fluorescent oligoDNA can discriminate one-base mismatched complement only when the mismatched base is positioned around the middle of the duplex-forming region.

Novel sequence-responding fluorescent oligoDNA probe bearing a silylated pyrene molecule.

A novel fluorescent phosphoramidite derivative of dimethylsilylated pyrene was prepared and incorporated into oligoDNA. The fluorescent oligoDNA exhibited marked fluorescent signal upon binding to the fully matched complementary DNA strand, however, the signal was strongly quenched in the single-stranded form as well as in the duplex having mismatched base pair at the terminus of the duplex-forming region.

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.

The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA(Tyr)s. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNA(Tyr)(GPsiA). Structural information for TyrRS-tRNA(Tyr) complexes is now full-line for three kingdoms.

Development of DNA-intercalator-polyamine multi-conjugate bearing the ability of the sequence-specific RNA hydrolysis.

A Novel anthraquinone-trisamine modified DNA conjugate was developed. The trisamine-bearing 2,7-disubstituted anthraquinone derivative was introduced into the central position of the DNA oligomer. The ability of the sequence-specific RNA cleavage of this novel modified DNA was investigated.

Synthesis and alternate-stranded triple helix forming ability of novel anthraquinone modified alpha-beta chimeric DNA.

A series of novel alpha-beta chimeric oligonucleotides bearing an anthraquinone-conjugated non-nucleosidic backbone were synthesized as a triplex-forming oligonucleotide (TFO). UV-melting experiments revealed that the obtained modified chimera TFOs form remarkably stable alternate-stranded triplex almost regardless to the stereochemistry of the incorporated non-nucleosidic backbone unit.

Synthesis and alternate-stranded triplex forming ability of novel alpha-beta chimeric oligonucleotides bearing an intercalator-conjugated nucleobase.

A series of novel alpha-beta chimeric oligonucleotides bearing anthraquinone-attached nucleobase at linker position, were synthesized as a triplex-forming oligonucleotide (TFO). Their ability to stabilize the alternate-stranded triple helix was investigated through the UV-melting experiments.

Synthesis and duplex-forming property of oligonucleotides bearing a novel polyamine-modified intercalator at the terminal or the internal position.

Novel oligonucleotides bearing a polyamine-intercalator conjugate modified at the terminal or the internal position were reported. These modified oligonucleotides showed duplex-stabilization effect, and the thermodynamic analysis and the salt concentration dependency of the duplex stability revealed that the polyamine moiety also acted as the duplex stabilizer by neutralization of the phosphate negative charge.

Crystallization and preliminary X-ray crystallographic analysis of yeast tyrosyl-tRNA synthetase complexed with its cognate tRNA.

Yeast tyrosyl-tRNA synthetase (yTyrRS) has been crystallized by the vapor diffusion method in the presence of its cognate tRNA(Tyr). The crystals belong to a tetragonal space group P4(1)2(1)2 with cell dimensions of a = b = 63.85 Angstrom, and c = 330.

Novel fluorescent oligoDNA probe bearing a multi-conjugated nucleoside with a fluorophore and a non-fluorescent intercalator as a quencher.

A set of 15mer linear oligoDNA probes bearing a modified nucleoside conjugated with a polyamine/fluorescein/anthraquinone reporting moiety were synthesized. In a single-stranded form, the fluorescence generated by the excitation of fluorescein was efficiently quenched, while marked recovery of the fluorescence was observed when the probes formed duplexes with the fully complementary strand.

Modified alpha-beta chimeric oligoDNA bearing a multi-conjugate of 2,2-bis(hydroxymethyl)propionic acid-anthraquinone-polyamine exhibited improved and stereo-nonspecific triplex-forming ability.

Novel alpha-beta chimeric oligonucleotides bearing a propionic acid derivative of an anthraquinone-polyamine conjugate in the "linker" region sequence-specifically formed a substantially stable alternate-stranded triplex with dsDNA almost regardless of the stereochemistry of the derivative.

Alpha-beta chimeric oligo-DNA bearing intercalator-conjugated nucleobase inside the linker sequence remarkably improves thermal stability of an alternate-stranded triple helix.

Novel alpha-beta chimeric oligodeoxynucleotides bearing an intercalator-conjugated nucleobase located at the internal 4-nt linker region were synthesized, and their triplex-stabilizing property was examined. The triple helical DNA formed between the modified chimera DNA and double-stranded DNA exhibited remarkable thermal stability; however, the position of the intercalator-conjugated nucleobase had little influence on the stability. Among the examined, modified chimera DNA bearing the two intercalator-conjugated nucleobases at adjacent positions exhibited the highest stability.

Novel anthraquinone conjugate of 2,2-bis(hydroxymethyl)propionic acid incorporated to a TFO with phosphodiester linkage facilitates triplex formation with dsDNA bearing a pyrimidine-gapped polypurine sequence.

An anthraquinone derivative conjugated with 2,2-bis(hydroxymethyl)propionic acid as a novel non-nucleosidic component was synthesized and successfully incorporated into an internal region of 14-mer triplex-forming oligonucleotide (TFO) via the phosphoramidite method. The resulted novel TFO exhibits remarkable enhancement effect on the thermal stability of a DNA triplex upon binding to a pyrimidine-gap containing polyprurine sequence.

Synthesis of novel TFOs bearing an abasic portion and their triplex forming ability with a DNA duplex containing a pyrimidine-gapped polypurine strand.

Novel bi-functional anthraquinone phosphoramidite reagent was prepared from anthraquinolylethylenediamine and 2,2-bis(hydroxymethyl)propionic acid. The amidite reagent was incorporated into the middle position of oligoDNA consisting of pyrimidine residues, exclusively. The resulted oligoDNA was examined as the triple helix forming oligonucleotide (TFO) targeting a homopurine tract of a double helical DNA possessing a single pyrimidine-gap sequence.

Formation and stability of alternate-stranded triplex formed with alpha,beta-chimeric oligoDNA.

Chimeric oligoDNAs composed of alpha-anomeric oligonucleotide and beta-anomeric oligonucleotide with modified nucleobases and/or phosphodiester backbone are synthesized and their ability to form alternate-stranded triple helix with dsDNA was examined. Substitution of normal phosphodiester linkages with phosphorothioate linkages resulted in the prominent destabilization of the alternate-stranded triplex. Meanwhile, the introduction of cationic molecule or intercalative molecule at certain positions of the modified DNA was effective to increase the stability of the triplexes.

Alternate stranded triplex formation of chimeric DNA composed of tandem alpha- and beta-anomeric strands.

A chimeric oligoDNA composed of a natural beta-anomeric oligonucleotide portion and an unnatural alpha-anomeric oligonucleotide portion forms an alternate stranded triplex possessing enhanced thermal stability compared to the triplexes composed of the parental oligomers.

First synthesis and anticancer activity of phosmidosine and its related compounds.

This paper describes the first synthesis of phosmidosine and phosmidosine B, i.e., nucleotide antibiotics composed of 8-oxoadenosine and L-proline which are connected via a unique N-acyl phosphoramidate linkage.