Biomedical subjects

Takahiro Sakaue

Publications and source records attributed to Takahiro Sakaue.

9 recordsLinked to original sources

PubMed2006

On the formation of rings-on-a-string conformations in a single polyelectrolyte chain: A possible scenario.

Recent single-molecular observations have revealed that a single giant DNA molecule assumes (micro) phase separated structures upon the addition of condensing agents. Electron and atomic force microscopy have clearly shown the coexistence of ordered tori and disordered coil structures within a single DNA molecule. Motivated by these experimental findings, we theoretically investigated the collapse transition of a single polyelectrolyte chain driven by the addition of condensing guest molecules. We found that the transition behavior critically depends on the degree of the surviving charge inside the torus. When the torus is charged, even slightly, "rings-on-a-string" structures are expected for a sufficiently long chain, owing to the combinational entropy of segment state distribution along the chain and the unique property of the stability of charged torus.

Journal Article↗

PubMed2005

Helical superstructures of fullerene peapods and empty single-walled carbon nanotubes formed in water.

Aqueous dispersions of fullerene C70-filled carbon nanotubes (C70@SWNTs or peapods) and empty single-walled carbon nanotubes (empty SWNTs) were prepared with the aid of trimethyl-(2-oxo-2-pyrene-1-yl-ethyl)-ammonium bromide (1), which is a carbon nanotube solubilizer. This is the first report describing the preparation and characterization of the transparent dispersion/dissolution of the peapods. The UV-vis-near-IR spectra of C70@SWNTs-1 and empty SWNTs-1 were almost identical. We found by means of transmission electron microscopy and atomic force microscopy that the empty SWNTs and C70-peapods form helical nanostructures in the shapes of rings, irregular rings, lassos, handcuffs, catenanes, pseudorotaxanes, and figure-eight structures. The mechanism of the superstructure formation has been discussed in relation to the unique characteristics of stiff polymer chains with the aid of an off-lattice Monte Carlo simulation.

Journal Article↗

PubMed2005

Rings-on-a-string chain structure in DNA.

Using fluorescence microscopy (FM), which permits the observation of single molecules, we found that a pearling structure is generated on a single long DNA molecule upon the addition of a gemini (dimeric) surfactant. This pearling structure was further investigated by performing atomic force microscopy measurements on the same DNA molecules as observed by FM. These observations revealed that the pearling structure is composed of many rings that are interconnected by elongated coil parts along a single DNA molecule, i.e., rings-on-a-string structure. The mechanism of the formation of such an intrachain segregated structure in terms of microphase separation on a single polyelectrolyte chain is discussed.

Bacteriophage T4↗

PubMed2004

Unwrapping of DNA-protein complexes under external stretching.

A DNA-protein complex modeled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without a stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and dynamics of the unwrapping process by computer simulations and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered; i.e., there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent of nucleosome. There is a clear winding number, and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated with discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.

Biophysics↗

PubMed2004

Emergence of multiple tori structures in a single polyelectrolyte chain.

We investigated the collapsed structure of a weakly charged wormlike chain under a moderate concentration of 1:1 electrolyte solution. By assuming a torus as a grand state, we found that the size of a torus is determined by the balance between surface energy and electrostatic energy, which leads to a finite torus thickness almost independent of the chain contour length. Owing to this unique characteristic, a long charged wormlike chain forms multiple tori structure as a collapsed product, which is never seen with a neutral wormlike chain. These features were confirmed by a Monte Carlo simulation.

Journal Article↗

PubMed2004

Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules.

It has been established that in a dilute solution individual giant DNA molecules undergo a large discrete transition between an elongated coil state and a folded compact state. On the other hand, in concentrated solutions, DNA molecules assemble into various characteristic states, including multichain aggregate, liquid crystalline, ionic crystal, etc. In this study, we compared single-chain and multiple-chain events by observing individual chains using fluorescence microscopy. We used spermidine, SPD(3+), as a condensing agent for giant DNA. When the concentration of DNA is below 1 microM in base-pair units, individual DNA molecules exhibit a transition from an elongated state to a compact state. When the concentration of DNA is increased to 10 microM, a thick fiberlike assembly of multiple chains appears. AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains. The transition between single-chain compaction and bundle formation with multiple-chain assemblies was reproduced by a theoretical calculation.

Base Pairing↗

PubMed2004

The exchanger inhibitory peptide region-dependent inhibition of Na+/Ca2+ exchange by SN-6 [2-[4-(4-nitrobenzyloxy)benzyl]thiazolidine-4-carboxylic acid ethyl ester], a novel benzyloxyphenyl derivative.

We investigated the properties and interaction domains of SN-6 [2-[4-(4-nitrobenzyloxy)benzyl]thiazolidine-4-carboxylic acid ethyl ester], a newly synthesized and selective Na(+)/Ca(2+) exchange (NCX) inhibitor. SN-6 (0.3-30 microM) inhibited preferentially intracellular Na(+)-dependent (45)Ca(2+) uptake (i.e., the reverse mode) compared with extracellular Na(+)-dependent (45)Ca(2+) efflux (i.e., the forward mode) in NCX1-transfected fibroblasts. SN-6 was 3- to 5-fold more inhibitory to (45)Ca(2+) uptake in NCX1 (IC(50) = 2.9 microM) than to that in NCX2 or NCX3 but not to that in NCKX2. We searched for regions that may form the SN-6 receptor by NCX1/NCX3-chimeric analyses and determined that amino acid regions 73 to 108 and 193 to 230 in NCX1 are mostly responsible for the differential drug response between NCX1 and NCX3. Further site-directed mutagenesis revealed that double substitutions of Val227 and Tyr228 in NCX1, which exist within the exchanger inhibitory peptide (XIP) region, mimicked the different drug response. In addition, F213R, G833C, and N839A mutations in NCX1 resulted in loss of drug sensitivity. Exchangers with mutated XIP regions, which display either undetectable or accelerated Na(+)-dependent inactivation, had markedly reduced sensitivity or hypersensitivity to SN-6, respectively. Cell ATP depletion enhanced the inhibitory potency of SN-6. Therefore, SN-6 at lower doses (IC(50) = 0.63 microM) potently protected against hypoxia/reoxygenation-induced cell damage in renal tubular cells overexpressing NCX1, suggesting that this drug predominantly works under hypoxic/ischemic conditions. These properties of SN-6, which may be derived from its interaction with the XIP region, are advantageous to developing it as a new anti-ischemic drug.

Adenosine Triphosphate↗

PubMed2004

[Characterization of SN-6, a novel exchange inhibitor and its renal protective effect].

Recently, we developed 2-(4- [4-nitrobenzyloxy] benzyl) thiazolidine-4-carboxylic acid ethyl ester (SN-6), a newly synthesized and selective inhibitor of Na(+)/Ca(2+) exchanger. SN-6 is a selective inhibitor for the Ca(2+) influx mode of Na(+)/Ca(2+) exchanger. And this compound attenuated hypoxia/reoxygenation-induced renal tubular cell damage and ischemia/reperfusion-induced renal failure. These results suggest that SN-6 is expected to be pharmacological tools to study the roles of the exchanger and a new anti-ischemic drug.

Acute Kidney Injury↗

PubMed2003

The antioxidant ESeroS-GS inhibits NO production and prevents oxidative stress in astrocytes.

Within the central nervous system uncontrolled production of large amounts of nitric oxide (NO) by activated glial cells might be the common pathogenesis of several neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. In the present investigation, we measured the effect of a novel antioxidant gamma-L-glutamyl-S-[2-[[[3,4-dihydro-2,5,7,8-tetramethyl-2-(4,8,12-trimethyltridecyl)-2H-1-benzopyran-6-yl]oxy]carbonyl]-3-[[2-(1H-indol-3-yl)ethyl]amino]-3-oxopropyl]-L-cysteinyl-glycine sodium salt (ESeroS-GS) on NO production in cultured rat astrocytes. Upon stimulation with 1 microg/mL lipopolysaccharide plus 100 U/mL interferon-gamma which induced the expression of inducible nitric oxide synthase, cultured astrocytes generated large amounts of NO as measured by nitrite assay and ESR technique. The endogenous NO caused oxidative damage in astrocytes, which was confirmed by the accumulation of both cytosolic and extracellular peroxides, the decrease in the cellular glutathione level, and the formation of thiobarbituric acid reactive substrates. Production of endogenous NO resulted in cell death finally. Pretreatment with the novel antioxidant ESeroS-GS effectively decreased the expression of iNOS gene, inhibited the formation of endogenous NO, and prevented NO-induced oxidative damage and cell death in astrocytes. The results suggest that ESeroS-GS might be used as a potential agent for the prevention and therapy of diseases associated with the overproduction of NO by activated astrocytes.

Animals↗