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Biomedical subjects

Mitsunobu Nakamura

Publications and source records attributed to Mitsunobu Nakamura.

16 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↗
PubMed2006

A new model of focal cerebral ischemia in the miniature pig.

OBJECT: The purpose of this set of studies is to design a minimally invasive, reproducible stroke model in the gyrencephalic brain. This paper provides information on both surgical technique and methods of quantification of ischemic damage to both gray and white matter in the miniature pig. METHODS: Sixteen male miniature pigs were randomly divided into three groups and underwent transcranial surgery involving a frontotemporal approach with orbital rim osteotomy for permanent middle cerebral artery occlusion (MCAO; five animals), permanent internal carotid artery occlusion (ICAO; six animals), and a sham operation (five animals). Histological mapping and magnetic resonance (MR) imaging were used to delineate the areas of ischemic damage. The volumes of infarction measured directly from MR images were 16.2 +/- 1.1, 1.5 +/- 0.5, and 0.0 +/- 0.0 cm3 (mean +/- standard deviation [SD], p < 0.001) in the MCAO, ICAO, and sham-operated groups, respectively. The areas of ischemia identified through histological analysis and MR imaging showed a good correlation (r2 = 0.86, p < 0.0001). Immunohistochemical staining with an amyloid precursor protein (APP) antibody was used to evaluate axonal damage and calculate a total APP score for axonal damage of 44.8 +/- 2.9 in the MCAO, 13.2 +/- 6.6 in the ICAO, and 0.0 +/- 0.0 (mean +/- SD, p < 0.002) in the sham-operated animals. CONCLUSIONS: This new model of focal cerebral ischemia induces a reproducible amount of ischemic damage in both gray and white matter, and has significant utility for studies of the pathophysiology of ischemia in the gyrencephalic brain and for assessment of the therapeutic efficacy of drugs prior to the initiation of human clinical trials.

Animals↗
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

The detection and quantification of highly reactive oxygen species using the novel HPF fluorescence probe in a rat model of focal cerebral ischemia.

A novel fluorescence probe, 2-[6-(4'-hydroxy) phenoxy-3H-xanthen-3-on-9-yl] benzoic acid (HPF) was used to investigate the generation of highly reactive oxygen species (hROS) under ischemia both in vitro and in vivo. In the in vitro study, HT 22 cells were used to demonstrate that was predominantly detected in the cytoplasm, which coincides with the location of the mitochondria and then its HPF fluorescence gradually increased from 6 to 24 h due to glutamate induced oxidative stress. In the in vivo study, the permanent and transient middle cerebral artery occlusion (MCAO) was induced in rats. Brain slices were incubated in an artificial medium containing HPF. The area of enhanced HPF fluorescence existed in both the ischemic core and the peri-infarct area at 4h after MCAO in both permanent and transient MCAO models. The area extended beyond the boundary of the ischemic damage into biochemically viable tissue. The enhanced fluorescent intensity following transient MCAO was higher than that observed in the permanent MCAO model. Hydroxyl radical scavenger, MCI-186 significantly suppressed the enhanced fluorescence intensity. This study demonstrated that HPF has a high sensitivity and specificity for the detection of hROS in focal cerebral ischemia as well as in a cellular model of oxidative stress.

Animals↗
PubMed2005

Cyclophilin C-associated protein and cyclophilin C mRNA are upregulated in penumbral neurons and microglia after focal cerebral ischemia.

Immunophilin ligands, such as cyclosporin A and FK506, have neuroprotective effects in experimental stroke models, although the precise mechanism is unclear. Cyclophilin C-associated protein (CyCAP) is a natural cellular ligand for the immunophilin, cyclophilin C, and has a protective effect against endotoxins by downmodulating the proinflammatory response. Expressions of CyCAP and cyclophilin C mRNA in a rat middle cerebral artery (MCA) occlusion ischemia model were investigated by Northern blotting and in situ hybridization. Both CyCAP and cyclophilin C mRNAs were ubiquitously distributed in the neurons of the normal brain. Expression increased in neurons of the periinfarct zone up to 7 days after MCA occlusion. The neuronal distribution was confirmed by counterimmunostaining of NeuN. Both mRNAs were predominantly expressed in microglia of the ischemic core at 7 days, confirmed by immunostaining with the microglial marker, ED1. The quantification of CyCAP and cyclophilin C mRNAs at 7 days by Northern blot analysis showed the 8.5-fold increase (P<0.005, n=6) and 6.8-fold increase (P<0.005, n=6), respectively, in ischemic core compared with control. The coincidence of CyCAP and cyclophilin C expression in neurons and microglia suggests distinct roles in each cellular population. In particular, the early increase in penumbral neurons might be related to protection in periinfarct neurons.

Animals↗
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↗
PubMed2002

Substitution effect, absorption, and fluorescence behaviors of 11,12-benzo-1,7,10,13-tetraoxa-4-aza- cyclopentadec-11-ene (benzoaza-15-crown-5) derivatives upon cation complexation in solvent extraction.

Substitution effect, absorption, and fluorescence behaviors of some benzoaza-15-crown-5 derivatives upon cation complexation in solvent extraction were studied. The introduction of a substituent on the nitrogen atom in benzoaza-15-crown-5 enhanced extractabilities in the solvent extraction of aqueous alkali metal picrates. The nondonating substituents raised the cation selectivity for Na(+) over K(+), but the donating substituents reduced the cation selectivity. The absorption and fluorescence spectral behavior was different with the alkali metal cations.

Journal Article↗
PubMed1998

Intramolecular Binaphthyl Formation from Radical Cations of Tri-1-naphthyl Phosphate and Related Compounds in Photoinduced Electron-Transfer Reactions Sensitized by 9,10-Dicyanoanthracene.

The photoinduced electron transfer of tri-1-naphthyl phosphate and related compounds sensitized by 9,10-dicyanoanthracene (DCA) in acetonitrile produces 1,1'-binaphthyl and the corresponding biaryl. The quenching rate constant of the DCA fluorescence is calculated to be equal to the diffusion-controlled rate constant from the Stern-Volmer analysis and the fluorescence lifetime measurement. The free energy change calculated from the redox potentials and excitation energy of the singlet excited DCA indicates that the quenching process occurs exergonically to give the tri-1-naphthyl phosphate radical cation and DCA radical anion through electron transfer from tri-1-naphthyl phosphate to the singlet excited DCA at the diffusion-controlled rate. On the basis of spectroscopic and kinetic studies with laser flash photolysis, pulse radiolysis, and gamma-radiolysis, the radical cation of tri-1-naphthyl phosphate forms an intramolecular pi-dimer radical cation with face-to-face interaction between the two naphthyl groups within 8 ns of the electron pulse. The 1,1'-binaphthyl radical cation is eliminated at the rate constant of k(r) = 5.3 x 10(5) s(-)(1) from the intramolecular pi-dimer radical cation. Branching ratios of the reaction pathways are estimated for the reactive intermediates such as the tri-1-naphthyl phosphate radical cation and its intramolecular pi-dimer radical cation from the rate constants and quantum yields. The electron-withdrawing character of the P(O) group in the O-P(O)-O spacer is responsible for the elimination of the binaphthyl radical cation. The DCA-sensitized photoinduced electron-transfer reaction of the tri-1-naphthyl phosphate is compared with the direct photoreaction.

Journal Article↗
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↗