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Biomedical subjects

Akimitsu Okamoto

Publications and source records attributed to Akimitsu Okamoto.

At least 37 records · Page 2Linked to original sources
PubMed2005

Public-key system using DNA as a one-way function for key distribution.

Novel public-key system using DNA has been developed. To solve key distribution problem, the public-key cryptography system based on the one-way function has been developed. The message-encoded DNA hidden in dummies can be restored by PCR amplification, followed by sequencing. We used these operations as a one-way function, and constituted a novel method for the key distribution based on the public-key system using DNA. We will show the way of holding a key in common just between specific two persons.

Base Sequence↗
PubMed2005

Nile Red nucleoside: novel nucleoside analog with a fluorophore replacing the DNA base.

A solvatochromic dye is very useful in studies of local polarity and dynamics in biological systems. A novel solvatochromic chromophore, Nile Red beta-C-2'-deoxyriboside, has been synthesized to act as a photophysical probe, and incorporated site-selectively into an oligodeoxynucleotide. The absorption and fluorescence spectra of Nile Red nucleoside showed a remarkable sensitivity to the solvent polarity.

Deoxyribose↗
PubMed2005

Schiff base-mediated base pairing.

We here present a novel covalently linked base pair via Schiff base formation between 5-formyluracil (fU) and 5-aminocytosine (AmC). The formation of Schiff base remarkably increases thermal stability of the duplex DNA, whereas it completely dissociates upon heating at 90 degrees C. Neither AmC nor fU produces covalent linkage with other natural bases, and thus the pairing ability of AmC and fU is very specific.

Base Pairing↗
PubMed2005

SNPs typing by base-discriminating fluorescence DNA probe.

For the development of a novel SNP typing method using BDF (base-discriminating fluorescent) nucleosides in biological samples, we examined the detection of the single base alteration in BRCA1 gene with PCR products amplified by an asymmetric PCR. A combination of PyU- and PyC-containing BDF probes clearly facilitates the discrimination of not only A/G homozygous samples but also heterozygous samples. The present SNP typing method with BDF probes is a very powerful homogeneous assay that does not require a special device or time-consuming steps.

DNA Probes↗
PubMed2005

Genotyping with hole-transporting DNA self-assembled monolayer.

High-throughput DNA sensors capable of detecting single-base mismatches are required for the routine screening of genetic mutations and disease. A new strategy for the electrochemical detection of single-base mismatches in DNA has been developed based on hole transport through DNA self-assembled monolayers. We prepared hole-transporting DNA self-assembled monolayers. Their photocurrent measurements were carried out using amperometory. Large photocurrent was observed when the DNA duplex which constituted a hole-transporting DNA self-assembled monolayer had a full-matched sequence, whereas the photocurrent for a DNA duplex containing a mismatched base pair was much smaller.

Aldehyde Dehydrogenase↗
PubMed2005

Sequence-selective 5-methylcytosine oxidation for epigenotyping.

Methylation of DNA is an epigenetic modification that can play an important role in the control of gene expression in mammalian cells. The development of a simple and convenient method for site-specific discrimination of cytosine methylation is imperative for genomic studies. Here we report a facile method for distinguishing between cytosine and 5-methylcytosine. Osmium tetroxide caused the dihydroxylation of the C5-C6 double bond of 5-methylcytosine under an appropriate reaction conditions. The oxidation of 5-methylcytosine-containing target DNA was controlled by hybridization with a guide DNA. This technique facilitates the typing of cytosine methylation at a specific site of the target DNA.

5-Methylcytosine↗
PubMed2004

Photostimulated hole transport through a DNA duplex immobilized on a gold electrode.

Photostimulated hole transport through DNA duplexes immobilized on gold electrodes has been investigated. By modifying a gold electrode with a DNA duplex containing a photosensitizer, we have observed a sequence-dependent cathodic photocurrent. DNA acts as a good mediator for cathodic photocurrent when appropriate sequences are selected.

Anthraquinones↗
PubMed2004

Synthesis of an artificial hole-transporting nucleoside triphosphate, dMDATP, and its enzymatic incorporation into DNA.

We report on the enzymatic synthesis of DNA wires by successive incorporation of artificial nucleotides. We synthesized an efficient hole-transporting nucleoside triphosphate, d(MD)ATP, and have examined the screening of polymerases and reverse transcriptases for enzymatic incorporation of d(MD)ATP into DNA. We found that KOD Dash is an effective enzyme for the enzymatic synthesis of (MD)A-containing DNA. Furthermore, the efficiency of enzymatic incorporation was remarkably improved by the addition of manganese chloride. By applying the PCR method to the synthesis of DNA containing a run of (MD)A, the (MD)A run was amplified up to 6 x 10(6) times. (MD)A runs prepared by the enzymatic method exhibited a high hole-transporting ability.

Adenosine Triphosphate↗
PubMed2004

DNA logic gates.

A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.

Base Sequence↗
PubMed2004

Cytosine detection by a fluorescein-labeled probe containing base-discriminating fluorescent nucleobase.

We report on a new method for the detection of a base at a specific site in a DNA sequence by monitoring the fluorescence emission of fluorescein. To achieve this goal, we developed a new base-discriminating fluorescent (BDF) nucleobase, naphthodeazaadenine ((ND)A). The fluorescence spectrum of the duplex possessing a cytosine base as a complementary base of (ND)A showed a fluorescence peak at 383 nm when using an excitation wavelength of 350 nm. When the complementary base of (ND)A was one of the other bases, the fluorescence intensity was very low. The fluorescence emission spectrum of (ND)A overlapped with the fluorescence excitation spectrum of fluorescein in the wavelength range of 400-500 nm. Thus, we designed FRET-BDF probes containing (ND)A as the FRET donor and fluorescein as the acceptor. The interaction of these two fluorophores, which are separated by defined base pairs, allowed an efficient energy transfer that resulted in a dominant fluorescence emission of fluorescein at 520 nm when using an excitation wavelength of 350 nm. Fluorescence emission from FRET-BDF probes was observed only when the complementary base of (ND)A is C, thus achieving a clear distinction of a C base on the complementary DNA strand. However, the general utility of our method is limited due to the quenching of the (ND)A fluorescence by a G/C base pair flanking (ND)A.

Base Pairing↗
PubMed2004

Pyrene-labeled base-discriminating fluorescent DNA probes for homogeneous SNP typing.

This paper describes the design of novel base-discriminating fluorescent (BDF) nucleobases and their application to single nucleotide polymorphism (SNP) typing. We devised novel BDF nucleosides, (Py)U and (Py)C, which contain a pyrenecarboxamide chromophore connected by a propargyl linker. The fluorescence spectrum of the duplex containing a (Py)U/A base pair showed a strong emission at 397 nm on 327 nm excitation. In contrast, the fluorescence of duplexes containing (Py)U/N base pairs (N = C, G, or T) was considerably weaker. The proposed structure of the duplex containing a matched (Py)U/A base pair suggests that the high polarity near the pyrenecarboxamide group is responsible for the strong A-selective fluorescence emission. Moreover, the fluorescence of the duplex containing a (Py)U/A base pair was not quenched by a flanking C/G base pair. The fluorescence properties are quite different from previous BDF nucleobases, where fluorescence is quenchable by flanking C/G base pairs. The duplex containing the C derivative, (Py)C, selectively emitted fluorescence when the base opposite (Py)C was G. The drastic change of fluorescence intensity by the nature of the complementary base is extremely useful for SNP typing. (Py)U- and (Py)C-containing oligodeoxynucleotides acted as effective reporter probes for homogeneous SNP typing of DNA samples containing c-Ha-ras and BRCA2 SNP sites.

Amides↗
PubMed2004

A nucleobase that releases reporter tags upon DNA oxidation.

We have developed a novel nucleosbase, edaG, that efficiently releases various reporter units upon one-electron oxidation. The edaG-selective degradation of ODNs was achieved by various mild oxidizing agents. The oxidant-dependent molecular releasing technique is quite useful not only for DNA-based drug releasing systems but also for the detection of long-range hole transport through DNA without time-consuming analysis.

Biosensing Techniques↗
PubMed2004

Design of base-discriminating fluorescent (BDF) nucleobase for SNP typing.

We have devised novel pyrene-labeled BDF nucleosides, (Py)U, (Py)C, (Py)deazaA, and (Py)A. BDF probes containing these fluorescent nucleosides selectively emit fluorescence only when the base opposite the BDF base is a target base. Oligonucleotides containing these BDF nucleosides act as effective reporter probes for homogeneous SNP typing of DNA samples.

Fluorescent Dyes↗
PubMed2004

Development of a novel solvatochromic pyrimidine analog for probing local dielectric environment of DNA polymerase.

A novel uracil derivative tethering a solvatochromic chromophore, 6-dimethyl-2-acylnaphthalene (DAN), has been synthesized, and local dielectric constant in the recognition site of Klenow fragment (KF) has been investigated by steady-state fluorescence measurement using DNA substrates containing the solvatochromic uridine. Steady-state fluorescence measurements suggest that KF covers about 10 base pairs of the duplex DNA upstream of the primer terminus, and the vicinity of the incorporation site of triphosphate is the most hydrophobic environment.

Binding Sites↗