PubMed Health⌕ Search

Biomedical subjects

T Shimidzu

Publications and source records attributed to T Shimidzu.

16 recordsLinked to original sources
PubMed1992

Syntheses of oligonucleotide derivatives with P(V) porphyrin and their properties.

Two types of oligonucleotide derivatives which are substituted by P(V) porphyrin at the phosphorus atom of an internucleotidic linkage and at the 5'-terminal internucleotidic linkage via a spacer were synthesized (Fig. 1), and hybridization capabilities of them with complementary oligonucleotides were evaluated. A novel method for a sensing of oligonucleotide by the fluorescence quenching via photo-induced electron transfer between the P(V) porphyrin labeled oligonucleotide and pyrene-labeled one on the oligonucleotide template is reported.

Base Sequence↗
PubMed1991

Synthesis and properties of oligonucleotide derivative with P(V) porphyrin.

Oligonucleotide derivatives with a P(V)tetraphenylporphyrin at the internucleotidic phosphodiester linkage were synthesized. Their interactions with the complementary oligonucleotide and pyrene-labeled oligonucleotide were investigated. Fluorescence from the porphyrin moiety was strongly quenched by the addition of the pyrene-labeled oligonucleotide and the template oligonucleotide.

Base Sequence↗
PubMed1991

Oligonucleotides with bis-pyrene adduct in the backbone: syntheses and properties of intramolecular excimer forming probe.

2-(N-bis(2-pyrenylethyl)methyl-amino)ethanol (BPAE) was synthesized and its interaction with DNA was examined to explore the efficiency of intramolecular excimer forming probe. As a result the fluorescence of intramolecular excimer of BPAE disappeared with the addition of poly(dA)-poly(dT). This result suggests an unique type of probe with its introduction to oligonucleotide.

DNA↗
PubMed1990

Limited proteolysis of silkworm antitrypsin by several proteinases.

Silkworm antitrypsin (sw-AT) isolated from larval hemolymph was limitedly digested by Achromobacter lysylendopeptidase, alpha-chymotrypsin, subtilisin BPN', subtilisin Carlsberg, papain, or Pseudomonas elastase. Each proteinase could cleave specific site(s) around the reactive site identified for the reaction of sw-AT and bovine trypsin. Among these proteinases, only subtilisin BPN' was inhibited by sw-AT, although weakly. By the cleavable amino acid sequence in sw-AT, it was suggested that whether or not these proteinases were inhibited by sw-AT did not solely depend on their substrate specificities. The susceptibility to the attack of proteinase should indicate that this region is exposed on the molecular surface. The amino acid sequence in the COOH-terminal region slightly away from the reactive site in sw-AT had homology with that in the corresponding region of the serine proteinase inhibitor (serpin) group.

Amino Acid Sequence↗
PubMed1990

Single site proteolysis in silkworm antitrypsin causes structural changes in behavior against denaturing reagents.

Silkworm antitrypsin (sw-AT), which was thought to belong to serpin family, changed its behavior against denaturation after chymotryptic cleavage of a single peptide bond (Tyr-Val) two amino acids away from the reactive site for trypsin (Lys-Val). This chymotrypsin-modified sw-AT became resistant to denaturation by heat, sodium dodecyl sulfate, or guanidine hydrochloride, and this characteristic was evident in its circular dichroism spectrum. The modified sw-AT was also indigestible by S. aureus V8 protease. These facts should indicate a structural change from a stressed, unstable state to a stable one accompanying the cleavage of the single peptide bond in sw-AT. The stabilizing factor was in part attributed to the interaction of a COOH-terminal fragment (5 kDa) and an NH2-terminal one (36 kDa) in modified sw-AT.

Animals↗
PubMed1990

Oligonucleotides with pyrene fluorophore at the sugar fragment: synthesis and properties in binding to complementary polynucleotide.

Oligonucleotides with 1-pyrenylmethyl substituent at the designated sugar residue were synthesized by using 5'-dimethoxytrityl 2'-(1-pyrenylmethyl)uridine 3'-phosphorobisdiethylamidite 1. It was shown that the pyrene-oligonucleotides have enhanced affinity in binding to the complementary polynucleotide sequence. The fluorescence yield and life time of the pyrene-oligonucleotide was drastically enhanced when bound by the complementary polynucleotide.

Base Sequence↗
PubMed1990

Structure and properties of oligonucleotide analogs having phosphoramidate linkages.

The oligothymidylate analogs, having several stereo regular phosphoramidate linkages, were synthesized. Melting temperatures(Tm) of complexes of the analogs and poly(dA) were measured by spectroscopic method. The abilities of the analogs to form the complexes with poly(dA) depended on their P-chirality of their modified linkages: one of the chiral isomers formed stable complexes, but another isomer formed less stable complexes.

Amides↗
PubMed1989

Syntheses and properties of oligodeoxyribonucleotide analogues having diastereochemically pure phosphoramidate linkages.

The oligothymidilate analogues, having stereoregular and alternative phosphormorpholidate/phosphodiester backbone, were synthesized from the diastereochemically pure dimer blocks by phosphorbisamidite method. The phosphormorpholidate linkage of the oligothymidilate analogues were resistant to snake venom phosphodiesterase, and no cleavage of the phosphodiester linkage of the analogues were slowly cleaved by the nuclease was slow. The abilities of isomers to form the complexes with poly(dA) greatly depended on their structures.

Amides↗
PubMed1988

Sequence-defined dimer block synthesis from unprotected nucleoside.

mediates to synthesize the oligodeoxynucleotides have been synthesize otected nucleoside using morpholinophosphorditetrazolide. From these sequence-defined oligodeoxynucleotides were also synthesized. The gen is composed of following steps; a) reaction of 5'-O-protected nucleo orpholinophosphorditetrazolide (phosphitilation), b) reaction of the nucleoside phosphoramidite with the second nucleoside (condensation), ueous oxidation with t-BuOOH (oxidation). RE 1/hlp F2/cmt F3/ext F4/can F5/nxt F6/ins F7/up F8/dwn F9/fin

Indicators and Reagents↗
PubMed1986

An approach to DNA fragment synthesis from unprotected nucleoside.

Oligodeoxynucleotides have been synthesized from unprotected nucleoside by use of morpholinophosphordichloridite as a phosphorylating reagent. This procedure consists of three (in situ) steps; the reaction of 5'-O-protected deoxynucleotide with morpholinophosphordichloridite, the reaction of the resulting on active mononucleotide derivative with the second nucleoside, non-aqueous oxidation, and then removal of amino moiety at phosphate diester linkage.

Base Sequence↗
PubMed1985

A rapid synthesis of a DNA fragment using an unprotected nucleoside and a phosphine derivative.

A rapid synthesis of DNA fragment from unprotected nucleoside and phosphine derivative, morpholinophosphordichloridite, has been studied, demonstrating a d(T-T) and its amino-phosphonate derivative syntheses. A high selectivity of this reagent eliminates the protection of nucleoside hydroxyl groups. The P-N bond in the resulting dinucleoside phosphite can readily be converted to a phosphite triester with alcohol and to the corresponding aminophosphonate by a non-aqueous oxidation with m-chlorobenzoic acid. The P-N bond in the phosphate link is very stable and so provides a protection for the phosphoryl group which has many potential uses. Deprotection can be achieved by a simple treatment with NH2OH.

DNA↗
PubMed1984

A simple and convenient synthesis of 3'-5'- or 2'-5'-linked oligoribonucleotide by polymerization of unprotected ribonucleoside using phosphorus tris-azole.

Oligoribonucleotides have been synthesized directly from unprotected ribonucleosides by a chemical polymerization approach using phosphorus tris-azoles. The procedure involves two steps: (i) the reaction of unprotected ribonucleoside with phosphorus tris-azole and (ii) the in situ oxidation of the resulting phosphite with iodine and water. Several phosphorus tris-azoles were investigated for generating oligoribonucleotide chains. Phosphorus tris-azoles of which azoles are imidazole, 2-methylimidazole, and 2-ethyl-4-methylimidazole were found to be most effective. Uridine, adenosine, and cytidine oligonucleotides were obtained rapidly in high yields without any protection. The inter-ribonucleotidic linkage of the oligomers consists of 3'-5'- and 2'-5'-linkages. The linkage isomers were easily separated by a reverse phase column chromatography. The present approach provides a convenient and potentially useful method for preparing 3'-5'- or 2'-5'-linked oligoribonucleotides.

Animals↗
PubMed1979

Synthesis of cationic cyclo-oligo(ethyleneadenine).

A novel cationic and cyclic oligo (ethyleneadenine) whose main chain has adenine ring was synthesized by the thermal polymerization of 9-(2-bromoethyl) adenine, in the solid phase. The chain extends through N-9 - N-1 and N-9 - N-7 of the adenine rings. Its molecular weight was determined to be 3960 by the sedimentation method. The micro-structure was confirmed mainly with NMR measurements. The cationic and cyclic oligo(ethyleneadenine) interacts with nucleotides and polynucleotides in neutral aqueous solution.

Adenine↗
PubMedDate not supplied

Synthesis and interactive properties of an oligonucleotide with anthraquinone at the sugar fragment.

The synthesis of a self-complementary oligonucleotide possessing an anthraquinonylmethyl substituent at the designated sugar fragment, 5'-CCU(2'AQ)AGCTAGG (1), is described. The anthraquinonylmethyl group was introduced to 2'-hydroxyl moiety of uridine, which was then converted to the protected phosphorobisdiethylamidite derivative. This reagent was used for the solid-phase synthesis of the modified oligonucleotide 1. The UV and CD melting behaviors indicate that the modified oligonucleotide 1 can form a duplex in aqueous buffer solution similar to the unmodified strand 5'-CCTAGCTAGG (7). The observed melting temperatures for the duplexes 1 and 7 were 57.4 and 40.0 degrees C, respectively. The temperature-dependent change in the intensity of the induced CD at around 335 nm reflected directly to the melting behaviors of duplex 1, indicating that the anthraquinone groups intercalate into the base pairs in the duplex. The intercalation-induced stability of the duplex translates into a free energy cost of 5.2 kcal/mol. The present work provides a novel method for enhancing the affinity of oligonucleotides for their complementary sequences.

Anthraquinones↗