Biomedical subjects

Kae Sato

Publications and source records attributed to Kae Sato.

12 recordsLinked to original sources

PubMed2005

Affinity capillary electrophoresis of DNA for detection of single-nucleotide polymorphisms and point mutations. Comprehensive study for optimization of the weak affinity.

A single-stranded DNA and its point mutant can be separated with affinity capillary electrophoresis (ACE) in which an appropriate ligand DNA is used as a pseudo-stationary affinity phase. In this paper, we systematically examine the effects of ligand sequence, capillary temperature, and cation concentration on the ACE separation quality, which is quantitatively evaluated in terms of resolution and peak height. For fine tuning of the affinity, control of MgCl(2) concentration and insertion of a spacer sequence into the ligand DNA are more effective than control of the capillary temperature. For design of the ligand DNA, a simple strategy is proposed, based on the prediction of melting temperature. This strategy was tested with eleven different sample sequences. All of them were separated under the same conditions (250 microM MgCl(2) and 25 degrees C), and nine cases of them had satisfactory separation qualities.

Cations↗

PubMed2005

Autonomous polymer loading and sample injection for microchip electrophoresis.

We have developed an extremely simple method for microchip electrophoresis. Loading of a sieving polymer solution and injection of a sample solution are autonomously executed by a microchip fabricated in poly(dimethylsiloxane) (PDMS). In advance, the energy for the fluid pumping is stored in bulk PDMS by evacuating air dissolved in PDMS, and the information for the sample plug regulation is coded into the microchannel design. Besides the simplicity, our method brings about an advantageous effect: sample compaction due to the discontinuous electrophoretic mobility at the sample/polymer interface. The sample compaction effect was moderate in ordinary size-dependent separation for double-stranded DNA and was extreme in affinity electrophoresis for single-stranded DNA (ssDNA). In the latter separation mode, ssDNA components were sequence-specifically separated by difference in affinity to a probe oligonucleotide immobilized to the sieving polymer matrix. We separated up to 60-mer ssDNA mixtures based on single-base substitutions. The separation processes included typically 100-fold sample compaction and were completed within 15-30 s. This technology provides easy, simple, and sensitive method for detection of gene point mutations and typing of single-nucleotide polymorphisms.

Base Sequence↗

PubMed2005

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

Aggregation of DNA-modified gold nanoparticles in a non-cross-linking configuration has extraordinary selectivity against terminal mismatch of the surface-bound duplex. In this paper, we demonstrate the utility of this selectivity for detection of single-base substitutions. The samples were prepared through standard protocols: DNA extraction, PCR amplification and single-base primer extension. Oligonucleotide-modified nanoparticles correctly responded to the unpurified products from the primer extension: aggregation for the full match and dispersion for all the mismatches. Applicability of this method to genomic DNA was tested with five human tumor cell lines, and verified by conventional technologies: mass spectrometry and direct sequencing. Unlike the existing methods for single-base substitution analysis, this method does not need specialized equipments, and opens up a new possibility of point-of-care diagnosis for single-nucleotide polymorphisms.

Biosensing Techniques↗

PubMed2005

Detection of single-base mutation by affinity capillary electrophoresis using a DNA-polyacrylamide conjugate.

We have developed an affinity capillary electrophoresis (ACE) method for detection of gene point mutations using a DNA-polyacrylamide conjugate as a pseudostationary affinity phase. In this study, the target DNA was prepared by mixing two PCR products: the wild type of K-ras gene and its codon 12 point mutant. The ligand DNA was designed to be complementary to codons 11 and 12 of the wild type. The target DNA was denatured by the addition of formamide and by heating at 95 degrees C for 5 min, and then electrophoretically separated by difference in affinity to the pseudoimmobilized ligand DNA. The method successfully separated a mixture of the wild-type DNA and each of six codon 12 point mutants by the same ligand DNA. The limit of mutation detection was determined by mixing the wild-type DNA with decreasing concentrations of the mutant DNA. The lowest level of detection was 10% mutant DNA in a background of the wild type. The practicability of this method has been confirmed using a colorectal carcinoma cell line. This study is the first demonstration of detection of gene point mutation in polymerase chain reaction (PCR) products using ACE, and opens up a new possibility of CE-based gene diagnosis.

Acrylic Resins↗

PubMed2005

Separation of 2-aminobenzoic acid-derivatized glycosaminoglycans and asparagine-linked glycans by capillary electrophoresis.

A capillary electrophoresis method was developed for the analysis of oligosaccharides combined with derivatization with 2-aminobenzoic acid. Glycosaminoglycan delta-disaccharides were effectively resolved on a fused-silica capillary tube using 150 mM borate, pH 8.5, as a running electrolyte solution. This analytical method was applied to the identification of glycosaminoglycan in combination with enzymatic digestion. The separation of N-glycans or glucose-oligomers was performed with a phosphate buffer containing polyethylene glycol or borate as an electrolyte solution. This method is expected to be useful in the determination of oligosaccharide structures in a glycoprotein.

Animals↗

PubMed2004

Power-free poly(dimethylsiloxane) microfluidic devices for gold nanoparticle-based DNA analysis.

An extremely simple, power-free pumping method for poly(dimethylsiloxane)(PDMS) microfluidic devices is presented. By exploiting the high gas solubility of PDMS, the energy for the pumping is pre-stored in the degassed bulk PDMS, therefore no additional structures other than channels and reservoirs are required. In a Y-shaped microchannel with cross section of 100 microm width x 25 microm height, this method has provided flow rate of 0.5-2 nL s(-1), corresponding to linear velocity of 0.2-0.8 mm s(-1), with good reproducibility. As an application of the power-free pumping, gold nanoparticle-based DNA analysis, which does not rely on the cross-linking mechanism between nanoparticles, has been implemented in a microchannel with three inlets. Target 15mer DNA has been easily and unambiguously discriminated from its single-base substituted mutant. Instead of colorimetric detection in a conventional microtube, an alternative detection technique suitable for microdevices has been discovered-observation of deposition on the PDMS surfaces. The channel layout enabled two simultaneous DNA analyses at the two interfaces between the three laminar streams.

DNA↗

PubMed2004

Single-base mutation detection using neutravidin-modified polystyrene nanoparticle aggregation.

A single-base mutation assay using the non-crosslinking aggregation of neutravidin-modified polystyrene nanoparticles is described. This method requires only two steps: hybridization of biotinylated probe and sample DNAs, and then mixing with neutravidin-modified nanoparticles. The aggregation was detected within 20 min in total. A combination of the DNA non-crosslinking aggregation and biotin-avidin technology has allowed sufficient performance for the detection of single nucleotide polymorphisms.

Avidin↗

PubMed2003

Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization.

To date, aggregation of DNA-functionalized gold nanoparticles by hybridization of target DNA in a cross-linking configuration has been intensively studied. Here, we report that aggregation in a non-cross-linking configuration is also possible and is even better from the viewpoint of genetic analysis because of its speed and sensitivity. In this system, 15 nm diameter gold nanoparticles functionalized with (alkanethiol)-15mer DNA are hybridized to target 15mer DNA at room temperature. At high NaCl concentration (>/=0.5 M), hybridization with complementary target DNA induces nanoparticle aggregation based on the salting-out effect. The aggregation can be detected by a colorimetric change of the colloidal solution within 3 min. Furthermore, unusual sensitivity of this system for single-base mismatch at the terminus opposite to the anchored side has been discovered. In fact, target DNA with such a kind of mismatch does not induce the colorimetric change at all, while target DNA with single-base mismatch at the middle of it cannot be discriminated from the fully complementary target. This non-cross-linking aggregation system opens up a new possibility of rapid and reliable genetic analysis.

Acrylic Resins↗

PubMed2003

Separation of saccharides derivatized with 2-aminobenzoic acid by capillary electrophoresis and their structural consideration by nuclear magnetic resonance.

Saccharides including mono- and disaccharides were quantitatively derivatized with 2-aminobenzoic acid (2-AA). These derivatives were then separated by capillary zone electrophoresis with UV detection using 50mM sodium phosphate buffer as the running electrolyte solution. In particular, the saccharide derivatives with the same molecular weight as 2-AA aldohexoses (mannose and glucose) and 2-AA aldopentoses (ribose and xylose) were well separated. The underlying reasons for separation were explored by studying their structural data using 1H and 13C NMR. It was found that the configurational difference between their hydroxyl group at C2 or C3 could cause the difference in Stokes' radii between their molecules and thus lead to different electrophoretic mobilities. The correlation between the electrophoretic behavior of these carbohydrate derivatives and their structures was studied utilizing the calculated molecular models of the 2-AA-labeled mannose, glucose, ribose, and xylose.

Electrophoresis, Capillary↗

PubMed2002

Peptidomics-based approach reveals the secretion of the 29-residue COOH-terminal fragment of the putative tumor suppressor protein DMBT1 from pancreatic adenocarcinoma cell lines.

Deleted in malignant brain tumors 1 is a putative tumor suppressor protein in brain, lung, esophageal,gastric, and colorectal cancer. Here we report the mass spectrometric identification of a 3335 Da peptide, which was found in serum-free conditioned medium from 5 of 15 pancreatic adenocarcinoma cell lines but not from 35 carcinoma cell lines and 2 nonmalignant pancreatic duct cell lines. The peptide was the 29 COOH-terminal amino acids from deleted in malignant brain tumors 1. It is suggested that the peptide is generated inside the cells by limited proteolysis and extracellularly secreted. Our peptidomics-based approach will help screen candidate marker peptides for a particular type of cancer.

Adenocarcinoma↗

PubMed2002

Single-cell analysis by a scanning thermal lens microscope with a microchip: direct monitoring of cytochrome c distribution during apoptosis process.

We developed a microsystem for cell experiments consisting of a scanning thermal lens microscope detection system and a cell culture microchip. The microchip system was good for liquid control in microspace, and this results in secure cell stimulation and coincident in vivo observation of the cell responses. The system could detect nonfluorescent biological substances with extremely high sensitivity without any labeling materials and had a high spatial resolution of approximately 1 microm. This system was applied to monitoring of cytochrome c distribution in a neuroblastoma-glioma hybrid cell cultured in the microflask (1 mm x 10 mm x 0.1 mm; 1 microL) fabricated in a glass microchip. Cytochrome c release from mitochondria to cytosol during the apoptosis process was successfully monitored with this system. The cytochrome c detected with this system was estimated to be approximately 10 zmol. We concluded that the system was suitable for measuring the distribution of chemical substances in a single cell because the microchip is good for liquid handling in microspace and the thermal lens microscope has high sensitivity and spatial resolution.

Apoptosis↗

PubMed2002

Peptide differential display of serum-free conditioned medium from cancer cell lines.

Conditioned medium (CM) from cultured cells is a source for screening small peptides of therapeutic or diagnostic value in cancer research. Mass spectrometry has recently enabled the profiling of peptides present in biological samples. We report a single-step extraction method to increase a chance to discover small peptides with a starting volume of 750 microl of serum-free CM. In combination with protein chip mass spectrometry, our protocol will contribute to the discovery of target peptides.

Chromatography, Ion Exchange↗