Amplification-free detection of bacterial genes using a signaling probe-based DNA microarray.

In this study, we developed a novel DNA microarray system that does not require fluorophore-labeling, amplification, or washing of the target nucleic acid fragments. Two types of DNA probes (so-called "signaling probes") labeled with a fluorescence dye (Cy3) and quencher molecule (BHQ2) were spotted on the DNA microarray such that fluorescent signals of Cy3 could be quenched by BHQ2 due to duplex formation between the probes. The addition of the target DNA or RNA fragments disrupted the duplex formed by the probes, resulting in the generation of fluorescence signals. We examined the assay conditions of the signaling probe-based DNA microarray, including the design of the probes, hybridization temperatures, and methods for fragmentation of target molecules. Since this approach does not require time-consuming processes, including labeling, amplification, and washing, the assay achieved specific detection of 16S rDNA and 16S rRNA extracted from Escherichia coli within 60 min, which was significantly rapid compared to conventional PCR-dependent DNA microarrays.

DNA recovery from a single bacterial cell using charge-reversible magnetic nanoparticles.

Highly efficient DNA recovery from a single bacterial cell was performed by means of imidazole-modified magnetic nanoparticles (Imi-MNPs). The modification by imidazole was confirmed by Fourier transform infrared spectroscopy. The Imi-MNPs were highly efficient at DNA extraction owing to the charge-reversible properties of Imi-MNPs, whereby DNA is attached to the particles at low pH and eluted at high pH because of electrostatic interactions. The DNA recovery ratio was determined by real-time PCR, and it revealed that complete recovery was guaranteed at ≥10(3) genome copies of Bacillus subtilis. Extraction of DNA from single bacterial cells was followed by PCR amplification of 16S rDNA and capillary electrophoresis. We achieved detection of single bacterial cells with a detection rate of 80%. We believe that our DNA recovery strategy may serve as a powerful tool for efficient DNA extraction and should be useful for quality control of cosmetics, foods, and pharmaceutical products.

Development of thin-film tunable band-pass filters based hyper-spectral imaging system applied for both surface enhanced Raman scattering and plasmon resonance Rayleigh scattering.

We describe the development of a hyper-spectral imaging (HSI) system composed of thin-film tunable band-pass filters (TF-TBPFs) and its application to inhomogeneous sample surfaces. Compared with existing HSI systems, the system has a simpler optical arrangement and has an optical transmittance of up to 80% owing to polarization independence. The HSI system exhibits a constant spectral resolution over a spectral window of 80 nm (530 to 610 nm) and tunable spectral resolution from 1.5 to 3.0 nm, and requires only 5.4 s per measurement. Plasmon resonance and surface enhanced Raman scattering (SERS) from inhomogeneous surfaces dispersed with Ag nanoparticles (NP) have been measured with the HSI system. The measurement of multiple Ag NPs is consistent with conventional isolated NP measurements as explained by the electromagnetic mechanism of SERS, demonstrating the validity of the HSI system.

Characterization of magnetic nanoparticles modified with thiol functionalized PAMAM dendron for DNA recovery.

Magnetic nanoparticles (MNPs) modified with the thiol functionalized polyamidoamine (PAMAM) dendron were synthesized to estimate their DNA recovery capabilities. Aminosilane-modified MNPs and MNPs surrounded by a phospholipid (distearoylphosphatidylethanolamine (DSPE)) bilayer were used as core particles. Cystamine-core PAMAM dendrimers were reduced by dithiothreitol to dendron thiols and chemically conjugated to the core particles. Characterization of the synthesis revealed an increase of the surface amine charge from generation 1 (G1) to G6, starting with an aminosilane initiator. Particle size distribution analysis indicated that G6 PAMAM-modified MNPs exhibited monodispersity in an aqueous solution. G6 PAMAM-MNPs and G6 PAMAM-PE-MNPs synthesized by the proposed method have equivalent DNA recovery abilities to PAMAM-MNPs prepared by the conventional divergent synthesis method. In optimized conditions, 96% of λDNA was recovered using G6 PAMAM-PE-MNPs. Therefore, the method for preparing PAMAM-MNPs and PAMAM-PE-MNPs proposed in this study will be a novel approach for producing DNA carriers for efficient DNA purification by magnetic separation.

Real-time detection of DNA hybridization on microarray using a CCD-based imaging system equipped with a rotated microlens array disk.

This work describes a novel charge-coupled device (CCD)-based imaging system (MB Biochip Reader™) for real-time detection of DNA hybridization to DNA microarrays. The MB Biochip Reader™ consisted of a laser light source (532 nm), a microlens array for generation of a multi-beam laser, and a CCD for 2-D signal imaging. The MB Biochip Reader™ with a rotated microlens array, allowed large-field imaging (6.2 mm × 7.6 mm with 6.45 µm resolution) with fast time-resolution at 0.2 s without speckle noise. Furthermore, real-time detection of DNA hybridization, which is sufficient to obtain accurate data from tens of thousands of array element per field, was successfully performed without the need for laser scanning. The performance of the MB Biochip Reader™ for DNA microarray imaging was similar to the commercially available photomultiplier tube (PMT)-based microarray scanner, ScanArray Lite. The system potentially could be applied toward real-time analysis in many other fluorescent techniques in addition to real-time DNA microarray analysis.

Difference in propagation of Ca2+ release in atrial and ventricular myocytes.

Intracellular [Ca2+] ([Ca2+]i) was imaged in atrial and ventricular rat myocytes by means of a high-speed Nipkow confocal microscope. Atrial myocytes with an absent t-tubule system on 8-di- ANEPPS staining showed an initial rise in Ca2+ at the periphery of the cell, which propagated to the interior of the cell. Ventricular myocytes showed a uniform rise in [Ca2+]i after electrical stimulation, consistent with a prominent t-tubular network. In atrial myocytes, there was a much shorter time between the peak of the [Ca2+]i transient and the peak contraction as compared to ventricular myocytes. A regional release of Ca2+ induced by an exposure of one end of the myocyte to caffeine with a rapid solution switcher resulted in a uniform propagation of Ca2+ down the length of the cell in atrial myocytes, but we found no propagation in ventricular myocytes. A staining with rhodamine 123 indicated a much greater density of mitochondria in ventricular myocytes than in atrial myocytes. Thus the atrial myocytes display a lack of "local control" of Ca2+ release, with propagation after the Ca2+ release at the periphery induced by stimulation or at one end of the cell induced by exposure to caffeine. Ventricular myocytes showed the presence of local control, as indicated by an absence of the propagation of a local caffeine-induced Ca2+ transient. We suggest that this finding, as well as a reduced delay between the peak of the [Ca2+]i transient and the peak shortening in atrial myocytes, could be due in part to reduced Ca2+ buffering provided by mitochondria in atrial myocytes as opposed to ventricular myocytes.

High-speed 1-frame/ms scanning confocal microscope with a microlens and Nipkow disks.

We have developed a high-speed confocal laser microscope. A microlens-array disk set in front of a pinhole-array disk improved optical efficiency more than ten times compared with that of conventional Nipkow confocal microscopy. This new microscope achieves a high-speed measurement of 1 frame/ms. We expect that it will be used for measuring biological and industrial active samples.