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Biomedical subjects

Akimitsu Okamoto

Publications and source records attributed to Akimitsu Okamoto.

At least 55 records · Page 3Linked to original sources
PubMed2004

Electrochemical behavior of gold electrodes modified with photosensitizer-tethered DNA.

We investigated electrochemical characteristics of gold electrodes modified with photosensitizer-tethered DNA. We synthesized 3'-thiol-modified DNA strands (ODN-SH) and 3'-anthraquinone-modified DNA strands (AQ-ODN). We prepared an AQ-ODN/ODN-SH duplex-modified electrode through hybridization of AQ-ODN with ODN-SH on the gold electrode. We used an amperometric technique for its photocurrent measurement. The large photocurrent was observed by irradiation of a DNA modified electrode at 365 nm. We also measured photocurrent with different DNA sequences on gold electrodes.

DNA↗
PubMed2004

Fluorescent probe for the detection of DNA conformational transition.

Two pyrene-labeled bases, (py)C and (8py)G, have been synthesized and incorporated into d(CG)n. In the CD spectra, structural transition of a modified oligodeoxynucleotide (ODN-Py) from B-form to Z-form has been observed under different salt concentrations. The conformational transition of ODN-Py was monitored by the change of emission wavelengths based on exciplex and monomer fluorescence of (py)C and (8py)G.

Cytosine↗
PubMed2004

Synthesis and fluorescence properties of oligonucleotides containing pyrene-dimethylaniline chromophore.

The photophysical properties of DNA oligomers containing novel uracil derivatives tethering a solvatochromic pyrene-dimethylaniline (Py-DMA) chromophore were investigated. In the steady-state fluorescence measurements of the modified DNA oligomer, dual fluorescence, originating from a locally excited (LE) and a twisted intramolecular charge transfer (TICT) state, was observed.

Aniline Compounds↗
PubMed2003

P-loop catalytically assisting the enzymatic cleavage of single-stranded DNA.

We demonstrated that a P-loop, a looped complex formed inside duplex DNA by adding peptide nucleic acids (PNA), acts catalytically as a template for enzymatic cleavage of single-stranded probe oligodeoxynucleotides (ODN). A PD-loop complex formed from P-loop and probe ODN was digested efficiently by a restriction enzyme, and the truncated probe ODN was released. The P-loop nicked by the enzyme can form PD-loop again with another probe ODN, and then assisted the enzymatic cleavage of an excess of probe ODN. In addition, by using dumbbell-formed ODN as a probe ODN, the efficiency of the P-loop-assisted ODN cleavage was enhanced considerably as compared with that of linear ODN. Thus, the method utilizing P-loop will make it possible to amplify the sequence information of duplex DNA via a catalytic cleavage of probe ODNs.

Base Sequence↗
PubMed2003

Design of base-discriminating fluorescent nucleoside and its application to t/c SNP typing.

We report a novel method for base detection using a base-discriminating fluorescent (BDF) nucleoside. We developed BDF probes containing methoxybenzodeazaadenine MDA and methoxybenzodeazainosine MDI, which give strong fluorescence only when the base on the complementary strand is cytosine and thymine, respectively. Thus, the MDA- and MDI-containing ODNs can be used as a very effective BDF probe for the detection of single base alterations, such as SNPs and point mutations. The present method using BDF probes is a very powerful tool for SNP typing that does not require any enzymes and time-consuming steps, and can avoid hybridization errors. In addition, a combination of MDA- and MDI-containing BDF probes facilitates the T/C SNP typing of a heterozygous sample.

Adenine↗
PubMed2003

Rational design of a DNA wire possessing an extremely high hole transport ability.

DNA is a promising conductive biopolymer. However, there are problems that need to be solved to realize real DNA wires. These include the low efficiency of hole transport and the serious oxidative damage that can occur during hole transport. We have demonstrated a protocol for the design of a DNA wire that can effectively mediate hole transport that is not adversely affected by oxidation during hole transport through the DNA duplex. We have synthesized a stable and effective DNA wire by incorporating a designer nucleobase, benzodeazaadenine derivatives, which have lower oxidation potentials and wider stacking areas but are not decomposed during hole transport.

Adenine↗
PubMed2003

Clear distinction of purine bases on the complementary strand by a fluorescence change of a novel fluorescent nucleoside.

A new fluorescent nucleoside, benzopyridopyrimidine (BPP), which can sharply distinguish between A and G bases opposite BPP has been devised. The base-pairing degeneracy of BPP strongly contributes to the sharp fluorescence change that is dependent on the type of purine bases opposite BPP. The hybridization of an ODN probe containing BPP with a target DNA facilitates the judgment with the naked eye of the type of purine base located at a specific site on the target DNA. The BPP-containing ODN is a very effective probe for A/G SNP typing.

DNA↗
PubMed2003

15N NMR study on site-selective binding of metal ions to guanine runs in DNA: a good correlation with HOMO distribution.

15N NMR of DNA containing 15N-N7-enriched guanine (G) in the presence of paramagnetic ions (Mn(II) and Co(II)) was investigated. As the concentration of metal ion was increased, 15N NMR signals of the 5'G of GG and the middle G of GGG broadened site-selectively, indicating that electron-donating sites in G runs preferentially localize on the 5'G of GG and the middle G of GGG. The selectivity for G-metal ion interaction observed in this study was in good agreement with calculated HOMO distribution of G runs.

Cations, Divalent↗
PubMed2003

Development of the drug release system in hole transfer reaction through DNA.

DNA is known as a good hole carrier, and the application for a molecular wire has been studied. The efficiency of hole transfer was estimated as band intensity of phosphorimagery after electrophoresis in polyacrylamide gel. For the application of long-range hole transport through DNA to gene diagnosis and electrochemical technology, the hole transport without complicated and unwieldy analyzing processes is strongly desired. Herein, we developed novel nucleosides, which release various function units by oxidation. We synthesized novel nucleosides, which were designed based on the chemistry of an efficient hole trapping nucleoside 8-methoxy G.

DNA↗
PubMed2003

DNA nanomotor using duplex-quadruplex conformational transition.

For DNA nanomotor, we synthesized 8-Py-dG and incorporated it into d(T3G2)4 which can form quadruplex. We measured CD spectra for this ODN. The result suggested that this ODN was changed from quadruplex to duplex by the hybridization with the complementary strand. Further, this ODN had a very interesting property of fluorescence. The fluorescent intensity could be controlled whether the complementary strand was existed, or not.

Base Sequence↗
PubMed2003

Clear distinction of pyrimidine bases on the complementary strand by fluorescence change of novel fluorescent nucleosides.

New fluorescent nucleosides, methoxybenzodeazaadenine ((MD)A) and methoxybenzodeazainosine ((MD)I) which can sharply distinguish between C and T bases, respectably. The hybridization of an ODN probe containing (MD)A and (MD)I with a target DNA facilitates the judgment with the fluorescence spectra of the type of pyrimidine bases located at a specific site on the target DNA. The (MD)A- and (MD)I containing ODN are very effective probes for pyrimidine SNP typing.

Adenine↗
PubMed2003

Enzymatic ligation and extension of DNA wire.

The ODNs containing (MD)A, which effectively mediate hole transport, were enzymatically ligated, and photo-induced hole transport reaction proceeded efficiently through a ligated long duplex. The ligated duplex showed high hole transport efficiency.

Autoradiography↗
PubMed2002

Site-specific discrimination of Cytosine and 5-methylcytosine in duplex DNA by Peptide nucleic acids.

For site-specific discrimination of cytosine (C) and 5-methylcytosine (mC) in duplex DNA, we developed a new method using peptide nucleic acids (PNAs). The combination of a PNA-assisted DNA displacement complex and a fluorescein-labeled probe oligomer allowed the detection of mC at the defined sites in target DNA using a restriction enzyme. After treatment of the complex with a restriction enzyme, strong fluorescence emission was observed for the complex containing C at the target site, whereas the fluorescence intensity for the complex containing mC was extremely weak.

5-Methylcytosine↗
PubMed2002

2-Amino-7-deazaadenine forms stable base pairs with cytosine and thymine.

2-Amino-7-deazaadenine ((AD)A) was incorporated into oligodeoxynucleotides (ODN) and their base-pairing properties with natural nucleobases were investigated. In melting temperature (T(m)) experiments, the duplex containing an (AD)A/C base pair showed a high stability comparable to that containing (AD)A/T base pair. Destabilization of the duplex usually observed for existing degenerate bases was not observed. However, the incorporation efficiency of dCTP was only 1.8% for TTP in single-nucleotide insertion reactions using polymerase.

Adenine↗
PubMed2002

Modulation of remote DNA oxidation by hybridization with peptide nucleic acids (PNA).

We have examined the efficiency of DNA photooxidation in DNA/PNA duplex and DNA/(PNA)(2) triplex for the first time. DNA/PNA duplex was cleaved at GG steps by external riboflavin with high efficiency like specific GG cleavage in DNA/DNA duplex. However, the 5'G selectivity of the GG oxidation in DNA/PNA duplex was much lower than that observed in DNA/DNA duplex. Remote DNA oxidation of oxidant-tethered DNA/PNA duplex was considerably suppressed. In contrast, the formation of DNA/(PNA)(2) triplex by hybridization with two PNA strands completely inhibited the remote GG oxidation, indicating that PNA acts as an inhibition for remote oxidative DNA damage.

DNA↗