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Kazuki Tainaka

Publications and source records attributed to Kazuki Tainaka.

At least 19 recordsLinked to original sources
PubMed2006

Methylcytosine-selective fluorescence quenching by osmium complexation.

We report on the control of the emission from a fluorophore fixed on DNA using the methylcytosine-selective addition of an osmium-bipyridine complex. We have synthesized DNA modified by a microenvironment-sensitive fluorophore, 2-dimethylamino-6-acyl-naphthalene. The emission from the fluorophore tethered to a probe DNA was effectively quenched by a methylcytosine glycol-osmium-bipyridine triad, which was located in the immediate neighborhood of the fluorophore. The discrimination of the cytosine methylation status at a methylation hot spot in the p53 gene was also executed using a well-designed fluorescent DNA probe.

Animals↗
PubMed2006

Nile Red nucleoside: design of a solvatofluorochromic nucleoside as an indicator of micropolarity around DNA.

The fluorophore, Nile Red, effectively works as a polarity-sensitive fluorescence probe. We have designed a new nucleoside modified by Nile Red for examining the change in the polarity of the microenvironment surrounding DNA. We synthesized a Nile Red nucleoside (1), formed by replacing nucleobases with Nile Red, through the coupling of a 2-hydroxylated Nile Red derivative and 1,2-dideoxyglycan. This nucleoside showed a high solvatofluorochromicity. The fluorescence of 1 incorporated into DNA was greatly shifted to shorter wavelength by the addition of beta-cyclodextrin. The photophysical function of the Nile Red nucleoside will be a good optical indicator for monitoring the change in the micropolarity properties at a specific site on target sequences with interaction between DNA and DNA-binding molecules.

DNA↗
PubMed2006

Simple SNP typing assay using a base-discriminating fluorescent probe.

We have developed a new concept involving a single-step homogeneous method for single-nucleotide polymorphism (SNP) typing. In this method, a probe containing base-discriminating fluorescent (BDF) bases is added to a sample solution. BDF base-containing DNA usually shows only a weak fluorescence, but emits a strong blue fluorescence when it recognizes a target base at a specific site in a hybridized strand. By utilizing this feature, a simple mix-and-read SNP typing assay was achieved without any tedious probe-designing or washing processes for exclusion of hybridization error or any addition of DNA-modifying enzymes. This is very different from conventional methods. We simultaneously analyzed a number of samples with ease, with a high accuracy, using our BDF assay.

Base Sequence↗
PubMed2006

Development of bipyridine-modified nucleobase for methylcytosine-selective crosslink reaction.

Recently, we have reported a novel epigenotyping method utilizing methylcytosine (M)-selective modification through osmium oxidation at a specific site of a long sequence using the formation of a bulge structure by hybridization with a guide DNA. In the key step of this chemical modification, the coordination of bipyridine ligand to osmium tetroxide accelerated the formation of a stable complex (M-Os-ligand). Herein, we report the development of novel capture oligodeoxy-nucleotides (ODNs) containing a bipyridine-modified nucleobase for M-selective interstrand crosslinking through cyclic osmate formation. The crosslink formation resulted in a drastic increase in the melting temperature (T(m)) of the duplex.

5-Methylcytosine↗
PubMed2006

Synthesis and properties of novel PRODAN-labeled uridine.

We have developed a novel base-discriminating fluorescent (BDF) nucleoside, (PDN)U, which contains a PRODAN chromophore connected at the C-5 position of uracil. The Stokes shift (Deltanu) of (PDN)U was highly dependent on the local dielectric property around the fluorophore. On the excitation at 450 nm, the fluorescence spectrum of the duplex containing a (PDN)U/A base pair showed a strong emission at 520 nm. In contrast, the fluorescence intensities of duplexes containing "mismatched" (PDN)U/N base pairs (N = C, G, or T) were considerably lower. Furthermore, the drastic change of fluorescence intensity by the nature of the complementary base is useful for SNP typing.

2-Naphthylamine↗
PubMed2006

Development of novel PRODAN-labeled nucleosides as base-discriminating fluorescent probes.

We have developed a PRODAN-labeled uridine ((PDN)U), which contains a polarity-sensitive chromophore at the C-5 position of uracil. This paper describes the synthesis and fluorescent properties of oligodeoxy-nucleotides (ODNs) containing PRODAN-labeled nucleosides ((PDN)C, (PDN)A, and (PDN)G). PRODAN chromophore was attached to cytosine at the C-5 position and to purine bases at the C-8 position to extend into the major groove. When BDF probes containing a PRODAN-labeled nucleoside hybridize with a "full-matched" ODN, the fluorescence spectrum showed a strong emission around 520 nm on 450 nm excitation. In contrast, when PRODAN-labeled nucleoside analogs form a "mismatched" base pair, the fluorescence was weaker.

2-Naphthylamine↗
PubMed2006

Photochemical evaluation of dual fluorescence of a novel DNA groove binder.

We synthesized the fluorophore-tethered oligopeptide showing a dual fluorescence in water, and the ratiometric fluorescence change of the modified oligopeptide was induced by the binding to DNA. The equilibrium of the modified oligopeptide between two excited states, a locally excited (LE) state and an intramolecular charge transfer (ICT) state, was controlled depending to DNA structures.

DNA↗
PubMed2006

Fluorescence quenching by methylcytosine-metal complexation.

We report the control of fluorescence emission from the fluorophore fixed on DNA using the methylcytosine-selective addition of an osmium(VI)-bipyridine complex. We synthesized the DNA modified by a microenvironment-sensitive fluorophore, 2-dimethylamino-6-acylnaphthalene. The fluorescence from the fluorophore tethered to a probe DNA was effectively quenched by the addition of the osmium(VIII)-bipyridine to the methylcytosine which is located at the immediate neighborhood of the fluorophore. The discrimination of cytosine methylation status at the mutation hot spot in p53 gene was also executed using a well-designed fluorescent DNA probe.

2-Naphthylamine↗
PubMed2006

Development of electrochemical detection for methylcytosine and its application.

We report electrochemical detection of methylcytosine. We developed a bipyridine ligand possessing an amino linker. This ligand was used for methylcytosine-selective osmium oxidation and subsequent redox labeling. The DNA labeled methylcytosine selectively with anthraquinone showed the current signal through hybridization with a DNA probe fixed on a gold surface.

2,2'-Dipyridyl↗
PubMed2006

Luminescence properties of dual fluorescent pyrene derivatives used as DNA probe molecule.

We examined the dual fluorescence mechanism of 8-[4-(dimethylamino)phenyl]-N-2-propynyl-1-pyrenecarbox-amide (PyADMA) in polar solvent. The emission band appeared on the short wavelength side does not depend on the solvent polarity. On the other hand, the red shifted emission band depends on solvent polarity. On the face of it, the phenomenon is similar to intramolecular charge transfer (ICT) dynamics of 4-dimethylamino benzonitrile (DMABN). However, direct absorption band from ground state to ICT state is observed on the fluorescence excitation spectrum at room temperature. It is suggest that PyADMA would emit from both S(1) and S(2) state against the Kasha rule. On the other hand, we also examined the interaction between PyADMA and nucleoside which composing PyDMA-U in water solution. We found out that dynamics of excited states of PyADMA monomer is different from them of PyDMA-U.

Alkynes↗
PubMed2005

Monitoring DNA structures by dual fluorescence of pyrene derivatives.

We have developed a nucleotide modified by a pyrene derivative with dual fluorescence. The dual fluorescence of the fluorophore, which was incorporated into DNA, was effectively controlled at ambient temperature according to DNA structural status. Our nucleoside with dual fluorescence is effective as a conceptually new probe for monitoring DNA hybridization by the color change without multilabeling with fluorescent dyes.

DNA↗
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

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

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

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↗
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↗