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Toshihiro Ihara

Publications and source records attributed to Toshihiro Ihara.

12 recordsLinked to original sources
PubMed2006

Metal ion-directed cooperative DNA binding of small molecules.

Compound (1), which consists of an oxine and a pyridinium group, was synthesized as a metal-responsive DNA binding ligand. Two 1s coordinate to a Cu(II) to form a stable dimer (1(2)-Cu), even in the presence of DNA. The binding of 1 with sonicated calf thymus DNA was enhanced by ca. 10(3) times after forming the dimer; the binding constants were estimated to be 3.2 x 10(4)M(-1) and 2.4 x 10(7)M(-1) in the absence and the presence, respectively, of a half mole of Cu(II). The enormous acceleration of the binding is partly attributed to the generation of a dicationic charge by the formation of the dimer. High cooperativity between dimers could be also responsible; dimers would gather along the duplex as a template to form 1D spiral aggregates.

Animals↗
PubMed2006

Colorimetric allele analysis based on the DNA-directed cooperative formation of luminous lanthanide complexes.

We present the facile technique of colorimetric SNP analysis through DNA-templated cooperative complexation between a luminescent lanthanide ion (Ln(3+): Tb(3+) or Eu(3+)) and two ODN (oligodeoxyribonucleotide) conjugates carrying a metal chelator. Ethylenediaminetetraacetic acid (EDTA) and 1,10-phenanthrorine (phen) were covalently attached to ODNs to form the conjugate probes, capture and sensitizer probes, respectively. The sequences of the conjugates were designed so as to form a tandem duplex with a target with their auxiliary units facing each other, providing a microenvironment to accommodate Ln(3+). The capture probes for the wild-type (wt) and the mutant (mut) of thiopurine S-methyltransferase gene, were mixed with equimolar amounts of Tb(3+) and Eu(3+), respectively. Then both of the allele specific capture probe solutions and the sensitizer probe were added to three different solutions containing the targets, wt/wt (G/G), mut/mut (C/C), and wt/mut (G/C). The solutions emitted in green, red, and yellow, respectively; the colors were identified even by the naked eye.

Alleles↗
PubMed2005

Photochemical ligation between anthracene-DNA conjugates and its analytical application to gene analysis.

Anthracene readily forms photoadducts (anthracene dimers). The reaction generally requires close proximity and certain spatial alignment of both reaction partners. DNA could provide an ideal scaffold for accelerating the reaction, photocyclic addition. We synthesized a number of anthracene-DNA conjugates. The sequences of the conjugates, 5'AntODN and 3'AntODN, were designed to bind adjacent sequences of the template with the anthracene units directed such that they stacked with each other. The conjugates were only dimerized in the presence of the template by light irradiation. The efficiency of dimerization was dependent on the structure of the conjugates and affected by one-base displacement in the template sequence.

Anthracenes↗
PubMed2004

Photochemical ligation of DNA conjugates through anthracene cyclodimer formation and its fidelity to the template sequences.

Anthracene readily forms photoadducts, anthracene dimers, and this photodimerization reaction has been well characterized. In general, however, the reaction requires close proximity and certain spatial alignment of both reaction partners. DNA could provide an ideal scaffold for accelerating the photocyclic addition. We synthesized a number of anthracene-DNA conjugates. The sequences of the conjugates, 5'AntODNn and 3'AntODNn (the length of methylene linkers: n = 3 or 6), were designed to bind adjacent sequences of the template with the anthracene units directed such that they stacked with each other. The conjugates were only dimerized in the presence of the template by light irradiation. The efficiency was affected by one-base displacement in the template sequence.

Anthracenes↗
PubMed2004

Preparation of DNA-modified nanoparticles and preliminary study for colorimetric SNP analysis using their selective aggregations.

DNA-modified nanospheres were prepared by anchoring amino-terminated oligodeoxynucleotides (ODNs) with carboxylates onto a colored polystyrene sphere surface through amido bonds. About 220 ODN molecules were immobilized onto a nanosphere 40 nm in diameter. Preliminary studies using the microspheres with 1 microm diameter reveal that the specificity of hybridization was retained after modification. Three kinds of differently colored (RGB, red/green/blue) nanospheres bearing unique ODNs on their surface were prepared for detecting the p53 gene. Each ODN is complementary to a different part in the 45mer sample that is a part of a conservative region of the p53 gene containing one of the hot spots. In a binary system using spheres R and G, the wild-type 45mer made the aggregates with yellow emission as the result of mixing both colors. The mutant 45mer containing one nucleotide displacement did not give such aggregates with distinct colors. The study of fluorescence resonance energy transfer (FRET) showed that spheres R and G directly contact each other in the aggregates with the wild type. The RGB ternary system gave aggregates with specific colors corresponding to the added ODN samples, wild type or mutant. In addition, in the presence of both samples, all of the spheres formed aggregates with white emission as a consequence of mixing three primary colors of light. This means that the present technique should allow us to conduct an allele analysis.

Colorimetry↗
PubMed2004

Cooperative hybridization of DNA conjugates and its analytical application.

Anthracene readily forms photoadducts (anthracene dimers). This photodimerization reaction has been well characterized. However the reaction generally requires close proximity and certain spatial alignment of both reaction partners. DNA could provide an ideal scaffold for accelerating the photocyclic addition. We synthesized a number of anthracene-DNA conjugates. The sequences of the conjugates, 5'AntODN6 and 3'AntODN6, were designed to bind adjacent sequences of the template with the anthracene units directed such that they stacked with each other. The conjugates were only dimerized in the presence of the template by light irradiation. The efficiency was affected by one-base displacement in the template sequence.

Anthracenes↗
PubMed2003

Metal ion-directed outside binding of small DNA ligand.

DNA binding of the ligand bearing an oxine and a pyridinium group was regulated by coexisting Cu2+ over the binding constant range of three orders of magnitude. The ligands coordinated to Cu2+ to form a dimer and then cooperatively bound outside of DNA duplex to give the well-regulated 1-D structure along the DNA backbone.

DNA↗
PubMed2003

Highly enhanced duplex stability of dipyrido [3,2-a:2',3'-c] phenazine-modified oligonucleotide conjugate.

Dipyrido [3,2-a:2',3'-c] phenazine (DPPZ) or 1,10-phenanthroline (Phen) was tethered to the 5'-end of a short oligonucleotide (ODN) to generate two ODN conjugates. The conjugates formed stable duplexes with complementary 6 mer (d(TTAGGG)), which is one unit of telomeric repeats of human. The melting temperature of the duplex with DPPZ conjugate was higher than that of the corresponding duplex with unmodified 6 mer by 19.6 degrees C. This stabilization is enormous compared with those observed in other ODN conjugates reported previously. It would be attributed to the effective interaction of tethered heteroaromatic groups with DNA base stack of the duplex.

Oligonucleotides↗