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Kazushige Yamana

Publications and source records attributed to Kazushige Yamana.

18 recordsLinked to original sources
PubMed2006

Conformational changes of DNA by photoirradiation of DNA-bis(Zn(II)-cyclen)-azobenzene complex.

Bis(Zn(II)-cyclen)-azobenzene derivative, which has two Zn(II)-macrocyclic tetraamine complexes connected through azobenzene spacer, has been synthesized as a cross-linking agent fordoublestranded DNA in aqueous solution. The Zn(II)-cyclen derivative selectively binds to A-T base pairs producing complexes between the Zn(II)-cyclen moiety and the imide-deprotonated thymine with breaking A-T base pairs. The azobenzene spacer undergoes cis/trans photoisomerization in the complex between the Zn(II)-cyclen derivative and the DNA duplex. The conformation of the DNA remarkably changed by photoisomerization of the azobenzene linker, when the Zn(II)-cyclen derivative binds to the DNA duplex with an interstrand cross-linking manner

Azo Compounds↗
PubMed2006

Electrochemical detection of DNA single base mismatch by the use of strand exchange reaction.

The electrochemical method based on the strand exchange reaction (SER) for the detection of DNA single-base mismatch has been developed. Different electrochemical responses due to the slower SER rates for mismatch containing DNA than fully matched DNA were observed by using the redox-modified partial duplex DNA immobilized on gold electrode as an analytical probe.

Base Pair Mismatch↗
PubMed2006

Photoelectrochemical properties of pyrene modified DNA immobilized on gold electrode.

Self-assembled monolayers (SAMs) of pyrene-modified DNA were prepared on gold electrode and their photoelectrochemical properties were investigated. The cathodic photocurrent was generated by photoirradiation of the SAM in the presence of methyl viologen as an electron carrier. The photocurrent efficiency increased with increasing the distance between the pyrene and the gold substrate.

DNA↗
PubMed2005

Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference.

Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene-DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene-RNA/RNA and the pyrene-DNA/DNA duplexes.

Circular Dichroism↗
PubMed2005

Alignment of pyrene aromatics along RNA double helix.

Multiple pyrene modified RNA duplex exhibits pyrene excimer fluorescence. The pyrene excimer fluorescence is significantly enhanced with an increase in the number of incorporated pyrenes. The pyrenes in the RNA helically aggregate with partial pi-stacking along outside of double stranded helical backbone.

Fluorescent Dyes↗
PubMed2003

Detection of acceptor sites for antisense oligonucleotides on native folded RNA by fluorescence spectroscopy.

Antisense strategy has high potential for curing diseases and studying gene functions by suppressing the translation step. For the strategy, it is essential to detect acceptor sites of antisense molecules on mRNA under physiological conditions. We propose a new analytical method for the detection of acceptor sites of antisense molecules with high sensitivity. 2'-O-Methyloligoribonucleotide containing 2'-O-(1-pyrenylmethyl)uridine (OMUpy) was chosen as the fluorescence probe. The fluorescence intensity due to the pyrene in single-stranded OMUpy was scarcely observed. When OMUpy was hybridized with the complementary oligoRNA, the fluorescence intensity at 375 nm was remarkably increased. It was found that the increase was derived from the localization of the pyrene by the measurements of time-resolved fluorescence spectroscopy, CD and UV absorption spectra. These results suggest that the change of the fluorescence intensity of OMUpy can be a useful index to monitor hybridization. In this study, we chose Escherichia coli. 16S-rRNA as the model RNA and chose seven regions for probing by OMUpy based on the reported secondary structure of 16S-rRNA. The fluorescence intensity of an equimolar mixture of OMUpy with 16S-rRNA varied depending on the sequence. In particular, the increment in the system of OMUpy-8, which can hybridize with region 887-896 nt of 16S-rRNA, was most significant among the systems. These results indicated that the site targeted by OMUpy-8 was exposed to regulatory molecules, and suggest that the method presented here is useful to design antisense molecules.

Base Sequence↗
PubMed2003

Electrochemical detection of single-base mismatches in DNA by a redox-active intercalator conjugated oligonucleotide.

A simple and direct electrochemical detection of DNA single-base mismatches utilizing anthraquinone-modified oligonucleotides (AQ-ODNs) bound to gold electrodes has been described. By using the redox-active oligonucleotides, the redox-active center can be positioned at the desired base-pair pocket in double-helical DNA, enabling us to measure the charge transport between the redox-active center and the electrode that sandwich mismatched and full-matched base-pairs in double helix. AQ-ODNs immobilized on gold electrodes have been found to be useful in the electrochemical discrimination of hybrids containing a single-base mismatch from the one with fully matched bases.

Base Pair Mismatch↗
PubMedDate not supplied

Bis-pyrene-labeled oligonucleotides: sequence specificity of excimer and monomer fluorescence changes upon hybridization with DNA.

The design, synthesis, and properties of a new pyrene excimer-forming probe of DNA have been described. 2,2-(Aminomethyl)propanediol was converted by the reaction with 1-pyrenebutylic acid to bis-pyrene-modified propanediol as a fluorescent non-nucleosidic linker. The bis-pyrene-modified linker can be incorporated via phosphoramidite chemistry into the 5'-terminal or internal positions of oligonucleotides (ODNs). The terminally modified ODNs showed almost similar affinity for complementary DNA when compared with the corresponding unmodified ODNs. The duplexes containing the bis-pyrene in the main chain exhibited higher melting temperatures relative to the corresponding duplexes containing propanediol linker at the same position. The UV and CD spectral studies indicate that the stacking interactions between the pyrene and DNA bases occur in the internally modified duplex and do not in the terminally modified duplex. The bis-pyrene modified linker itself displays excimer (E at 480 nm) and monomer (M at 380 nm) emission in a quantum yield (QY) of 0.17 and the E/M intensity ratio of 15. Incorporation of this linker into the terminal or internal positions of ODNs reduced the QY (0.003-0.009) and the E/M ratio (0.3-0.8). While small changes in the QY and E/M ratio was obtained in binding of the internally labeled ODNs to DNA, up to 27-fold increase in the QY and 17-fold increase in the E/M ratio was observed upon hybridization of the terminally labeled ODNs with DNA. The excimer and monomer fluorescence changes were found to be sensitive to a mismatch base present in the target DNA. The bis-pyrene-modified ODNs thus provide a sequence-sepcific fluorescent probe of DNA.

Base Sequence↗