Mechanistic investigation of bead-based padlock rolling circle amplification under molecular crowding conditions.

We present a mechanistic investigation of bead-based padlock rolling circle amplification (RCA) under molecular crowding conditions, a sensitive and selective DNA detection method we have developed. Several important points to optimize the method were clarified: (i) the increase in the number of RCA products is proportional to the excluded volume of poly(ethylene glycol) (PEG), (ii) PEG facilitates ligation of padlock probe to form circular concatemers and monomers, both of which may act as a template for RCA, and (iii) hybridization of detection probe to the products may be facilitated at higher PEG concentrations.

Characterizing the non-crosslinked aggregation of DNA-modified gold nanoparticles: effects of DNA length and terminal base pair.

We previously reported that fully complementary DNA duplexes formed on gold nanoparticle (GNP) surfaces aggregate at high salt concentrations. We previously reported that DNA-functionalized gold nanoparticles (GNPs) aggregate by hybridization with fully complementary DNA at high salt concentrations. Although this behavior has been applied to some precise naked-eye colorimetric analyses of DNA-related molecules, the aggregation mechanism is still unclear and comprehensive studies are needed. In this paper, we reveal the key factors that influence GNP aggregation. The effects of temperature, electrolyte concentration, probe length, and particle size, which control the stabilities of double-stranded DNAs and GNPs, were investigated. Larger GNPs aggregated more easily, and GNP aggregates were easily formed with ∼15-mer-long probes, while longer probes prevented aggregation, perhaps by preventing the formation of rigid double-stranded DNA layers, compared to shorter probes. Furthermore, GNPs with purine bases at their 5' ends aggregated more easily than those with these bases at their 3' ends. This phenomenon is different from that based on the melting-temperature trend calculated using the nearest-neighbor method.

Molecular crowding improves bead-based padlock rolling circle amplification.

Bead-based padlock rolling circle amplification (RCA), an ultrasensitive and accurate DNA detection technique, was conducted in a molecular crowding environment created by poly(ethylene glycol) (PEG). The number of RCA products generated increased and exhibited a bell-shaped dependence on PEG concentration. Experiments using magnetic beads suggested that facilitation of DNA ligation and hybridization is the main reason for the observed increase. Selectivity of the technique was retained in the presence of PEG. This technique is simple and can be utilized to detect target DNA with high accuracy and sensitivity in a variety of areas such as medical diagnosis and food analysis.

Alternating current cloud point extraction on a microchip: the effect of electrode geometry.

We report on the effect of electrode geometry on alternating current cloud point extraction (ACPE). ACPE is a technique utilized to extract membrane-associated biomolecules in an electrode-integrated microfluidic channel. In this study, we investigated the effect of gap size (4∼22 µm) between microband electrodes on ACPE. A decrease in gap size resulted in efficient and rapid concentration of fluorescent-labeled phospholipids, a model of membrane-associated biomolecules. We also investigated the effect of applied voltage amplitude on ACPE using devices with decreased electrode gap size. When the gap was small, ACPE was achieved with low applied voltages. ACPE of membrane proteins extracted from HeLa cells was also studied to demonstrate the applicability of the ACPE to real samples. The results provide a guideline to improve the performance of ACPE and facilitate application of the ACPE technique as part of an overall analytical process.

Magnetic resonance imaging of a microvascular-interstitium model on a microfluidic device.

We report a microvascular-interstitium model on microfluidic devices to study leakage of drugs from blood vessels under in vivo-like flow conditions. We employed magnetic resonance imaging to demonstrate the compatibility of the model for experimental animals and humans. We observed transport of two types of different molecular-weight contrast agents into the model interstitium. The ratio of the transport rates of agents agreed with the ratio calculated from diffusion coefficients of the agents. We expect that the model will be useful for the estimation and evaluation of leakage of many kinds of agents in vivo.

Bead-based padlock rolling circle amplification for single DNA molecule counting.

Padlock rolling circle amplification (RCA) is a powerful analytical method for ultrasensitive DNA detection. Although there are some advantages to bead-based RCA, a detailed study of the relationship between the bead material and the efficiency of bead-based RCA has not been reported. Here, we compared the reaction efficiencies of bead-based RCA performed on two types of bead material: agarose and polystyrene. Agarose was a more suitable material for on-bead RCA. The calibration curve showed linearity between 0.05 and 1 nM, and the limit of detection was 9 pM (9 amol) for Salmonella DNA determination.

Gelatin-based cell culture device for construction and X-ray irradiation of a three-dimensional oral cancer model.

Bioassays using three-dimensional (3D) tissue models offer several advantages over 2D culture assays because they can reproduce the structure and function of native tissues. In this study, we used our newly designed gelatin device to generate a miniature 3D model of human oral squamous cell carcinoma with stroma and blood vessels. To enable air-liquid interface culture, we conceived a new device structure in which three wells were lined up and separated by a dividing thread; the wells could be connected by removing the dividing thread. Cells were seeded in the center well with the dividing thread to form a multilayer, followed by the supply of media from the side wells after thread removal. Human oral squamous cell carcinoma (HSC-4) cells, human umbilical vein endothelial cells (HUVECs), and normal human dermal fibroblasts (NHDFs) were successfully cocultured, resulting in structures that mimicked 3D-cancer tissues. This 3D-cancer model was subjected to an X-ray sensitivity assay, followed by the evaluation of DNA damage using confocal microscopy and section-scanning electron microscopy.

Alternating current cloud point extraction on a microchip: a comprehensive study.

We present a comprehensive study of alternating current cloud point extraction (ACPE) on a microchip. ACPE is an extraction technique for preconcentration of membrane-associated biomolecules. To characterize and optimize ACPE, we carried out ACPE experiments under various experimental conditions including amplitude and frequency of applied voltages, flow velocity, and concentration of surfactant, analyte, and salt. We found that ACPE has an amplitude threshold (15 V(p-p)), above which the extraction was more efficient. The dependence of the extraction on frequency (>5 MHz) was insignificant. Efficient extraction was achieved when the velocity of the test solution was 0.10∼0.67 mm s⁻¹ and the concentration of surfactant was 0.10∼1.0%. In contrast, the extraction was independent of the concentration of analytes (0.20∼20 µmol dm⁻³). The technique was applicable to solutions with a salt concentration of 0.050∼0.15 mol dm⁻³ under temperature control of the devices. Solution temperature in ACPE was also studied. These results provide guidelines for use of the ACPE technique in microfluidic chemical and biochemical analyses.

A palmtop-sized microfluidic cell culture system driven by a miniaturized infusion pump.

A palmtop-sized microfluidic cell culture system is presented. The system consists of a microfluidic device and a miniaturized infusion pump that possesses a reservoir of culture medium, an electrical control circuit, and an internal battery. The footprint of the system was downsized to 87 × 57 mm, which is, to the best of our knowledge, the smallest integrated cell culture system. Immortalized human microvascular endothelial cells (HMEC-1) and human umbilical vein endothelial cells (HUVEC) were cultured in the system. HMEC-1 in the system proliferated at the same speed as cells in a microchannel perfused by a syringe pump and cells in a culture flask. HUVEC in the system oriented along the direction of the fluid flow. Claudin-5, a tight junction protein, was localized along the peripheries of the HUVEC. We expect that the present system is applicable to various cell types as a stand-alone and easy-to-use system for microfluidic bioanalysis.

Fabrication of a Gelatin-Based Microdevice for Vascular Cell Culture.

This study presents a novel technique for fabricating microfluidic devices with microbial transglutaminase-gelatin gels instead of polydimethylsiloxane (PDMS), in which flow culture simulates blood flow and a capillary network is incorporated for assays of vascular permeability or angiogenesis. We developed a gelatin-based device with a coverslip as the bottom, which allows the use of high-magnification lenses with short working distances, and we observed the differences in cell dynamics on gelatin, glass, and PDMS surfaces. The tubes of the gelatin microfluidic channel are designed to be difficult to pull out of the inlet hole, making sample introduction easy, and the gelatin channel can be manipulated from the cell introduction to the flow culture steps in a manner comparable to that of a typical PDMS channel. Human umbilical vein endothelial cells (HUVECs) and normal human dermal fibroblasts (NHDFs) were successfully co-cultured, resulting in structures that mimicked blood vessels with inner diameters ranging from 10 µm to 500 µm. Immunostaining and scanning electron microscopy results showed that the affinity of fibronectin for gelatin was stronger than that for glass or PDMS, making gelatin a suitable substrate for cell adhesion. The ability for microscopic observation at high magnification and the ease of sample introduction make this device easier to use than conventional gelatin microfluidics, and the above-mentioned small modifications in the device structure are important points that improve its convenience as a cell assay device.

Single-molecule DNA patterning and detection by padlock probing and rolling circle amplification in microchannels for analysis of small sample volumes.

The rolling circle amplification (RCA) is a versatile DNA amplification method in which a DNA molecule is amplified using a single DNA primer, allowing the product to be counted as a single dot. Circular templates for RCA can arise from padlock probes in highly specific DNA target-mediated ligation reactions. However, improvement of detection efficiency represents an important challenge. In homogeneous assays, the detection efficiency is generally only under 0.1%, mainly because the sample volume is too large compared with the detection volume. Here, we used microchannel surfaces in a glass microchip for DNA detection in small volume samples. First, DNA patterning on glass surfaces in microchannels was demonstrated using chemical surface patterning by UV light. By using a photochemical reaction, we realized DNA patterning in a closed space. Second, RCA was demonstrated using dilutions of target molecules, and a calibration curve was obtained. The highest detection efficiency was 22.5% by virtue of the reduced sample volumes from several hundred microliters to 5.0 nL. Accordingly, a countable number of DNA molecules was successfully detected. This method is suitable for analysis of very small volume samples such as single cells, especially by using extended-nanochannels with dimensions of 10-1000 nm.

Bead-based Padlock Rolling Circle Amplification under Molecular Crowding Conditions: The Effects of Crowder Charge and Size.

Bead-based padlock rolling circle amplification under molecular crowding conditions, which we have developed for ultrasensitive detection of DNA, is examined to improve the detection efficiency and sensitivity of the method as well as to gain insight into the mechanism of the method. Both non-magnetic and magnetic sepharose microbeads were employed. Biotinylated DNA had to be pre-immobilized onto the microbeads in order to obtain products on the magnetic beads. The optimal concentration of biotinylated DNA was found to be about 5 µM, above which the number of products decreased. The effect of the crowder charge was examined, and neutral polymers were found to be effective on ligation and the hybridization step, while charged polymers were only effective on the hybridization step and inhibited the ligation and primer extension. The effect of the molecular weight of neutral dextran on the number of products was investigated, and the number of products was found to be increased with an increase in the molecular weight of dextran.

Microbead-based rolling circle amplification in a microchip for sensitive DNA detection.

The sensitive detection and quantification of DNA targets in the food industry and in environmental and clinical settings are issues of utmost importance in ensuring contamination-free food, monitoring the environment, and battling disease. Selective probes coupled with powerful amplification techniques are therefore of major interest. In this study, we set out to create an integrated microchemical chip that benefits from microfluidic chip technology in terms of sensitivity and a strong detection methodology provided jointly by padlock probes and rolling circle amplification (RCA). Here, we have integrated padlock probes and RCA into a microchip. The chip uses solid phase capture in a microchannel to enable washing cycles and decrease analytical area, and employs on-bead RCA for single-molecule amplification and detection. We investigated the effects of reagent concentration and amount of padlock probes, and demonstrated the feasibility of detecting Salmonella.

An efficient surface modification using 2-methacryloyloxyethyl phosphorylcholine to control cell attachment via photochemical reaction in a microchannel.

This report describes a direct approach for cell micropatterning in a closed glass microchannel. To control the cell adhesiveness inside the microchannel, the application of an external stimulus such as ultraviolet (UV) was indispensible. This technique focused on the use of a modified 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer, which is known to be a non-biofouling compound that is a photocleavable linker (PL), to localize cells via connection to an amino-terminated silanized surface. Using UV light illumination, the MPC polymer was selectively eliminated by photochemical reaction that controlled the cell attachment inside the microchannel. For suitable cell micropatterning in a microchannel, the optimal UV illumination time and concentration for cell suspension were investigated. After selective removal of the MPC polymer through the photomask, MC-3T3 E1 cells and vascular endothelial cells (ECs) were localized only to the UV-exposed area. In addition, the stability of patterned ECs was also confirmed by culturing for 2 weeks in a microchannel under flow conditions. Furthermore, we employed two different types of cells inside the same microchannel through multiple removal of the MPC polymer. ECs and Piccells were localized in both the upper and down streams of the microchannel, respectively. When the ECs were stimulated by adenosine triphosphate (ATP), NO was secreted from the ECs and could be detected by fluorescence resonance energy transfer (FRET) in Piccells, which is a cell-based NO indicator. This technique can be a powerful tool for analyzing cell interaction research.

Micro OS-ELISA: Rapid noncompetitive detection of a small biomarker peptide by open-sandwich enzyme-linked immunosorbent assay (OS-ELISA) integrated into microfluidic device.

A novel detection system that combines the merits of open-sandwich (OS) enzyme-linked immunoadsorbent assay (ELISA) and a microfluidic sensor chip system, and which enables rapid and noncompetitive immunodetection of small antigens of less than 1000 in molecular weight, has been proposed. Equipped with a sensitive thermal lens microscope, a minute amount of the carboxyl-terminal peptide of human osteocalcin (BGP), a biomarker for bone metabolism, was quantified utilizing antigen-dependent stabilization of an antibody variable region (OS principle). In a short analysis time (approximately 12 min), we could attain a detection limit comparable to that of the microplate-based OS ELISA (1 microg L(-1)). In addition, the effects of several pretreatments for serum-derived samples were investigated: an albumin absorption resin, addition of a protease inhibitor cocktail and heat treatment. Each pretreatment was found to be effective. Consequently, intrinsic BGP and its fragments could be detected in healthy human serum with a superior detection limit and working range compared to those of the conventional competitive ELISA method.

Nitric Oxide and a Conditioned Medium Affect the Hematopoietic Development in a Microfluidic Mouse Embryonic Stem Cell/OP9 Co-Cultivation System.

A microfluidic co-culture system, consisting of mouse embryonic stem cells (mESCs)/OP9 cells, was evaluated as a platform for studying hematopoietic differentiation mechanisms in vitro. mESC differentiation into blood cells was achieved in a microchannel that had the minimum size necessary to culture cells. The number of generated blood cells increased or decreased based on the nitric oxide (NO) donor or inhibitor used. Conditioned medium from OP9 cell cultures also promoted an increase in the number of blood cells. The number of generated blood cells under normal medium flow conditions was lower than that observed under the static condition. However, when using a conditioned medium, the number of generated blood cells under flow conditions was the same as that observed under the static condition. We conclude that secreted molecules from OP9 cells have a large influence on the differentiation of mESCs into blood cells. This is the first report of a microfluidic mESC/OP9 co-culture system that can contribute to highly detailed hematopoietic research studies by mimicking the cellular environment.

A micro-ELISA system for the rapid and sensitive measurement of total and specific immunoglobulin E and clinical application to allergy diagnosis.

We have developed a novel, practical micro-ELISA system for sensitive and rapid allergy diagnosis. The enzymatic reactions occurred under stopped-flow conditions, resulting in both high precision and high sensitivity. A BSA-biotin-avidin linker was introduced for the immobilization of water-soluble allergens on polystyrene microbeads, enabling immobilization of allergens in sufficient density to provide high sensitivity. Evaluation of the system's performance showed a good detection limit (2 ng/mL) for total IgE measurement. In addition, a good correlation with a conventional method (CAP method) was demonstrated using human serum samples from 85 allergy patients. Importantly, sample volumes (5 microL) were 10 times smaller and analysis time (12 min) was >20 times faster than the conventional method. All procedures were automatically regulated with our simple microfluidic system, and all the fluidic, optic and electronic components were integrated for portability. We believe that our system has the potential to become a very powerful tool, particularly for point-of-care diagnosis.

Serial DNA immobilization in micro- and extended nanospace channels.

That focused arrays, even with a small set of ligands, provide more data than single point experiments is well established in the DNA microarray research field, but microarray technology has yet to be transferred to fused silica microchips. Fused silica microchips have several attractive features such as stability to pressure, solvents, acids and bases, and can be fabricated with minute dimensions, making them good candidates for nanofluidic research. However, due to harsh bonding conditions, DNA ligands must be immobilized after fabrication, thus preventing standard microarray spotting techniques from being used. In this paper, we provide tools for serial DNA immobilization in fused silica microchips using UV. We report the synthesis of a new UV-linker which was used to covalently couple functional DNA oligos to the inside of channels in fused silica microchips. With some simple modifications to our mask aligner, we were able to transfer OHP mask patterns, which allows the creation of basically any pattern in the channels. The functionality of the oligos was measured through the binding of fluorophore-labeled complementary target oligos. We examined parameters influencing DNA immobilization, and carry-over between spots after consecutive immobilizations inside the same channel. We also report the first successful multiple immobilizations of functional DNA oligos inside single channels of extended nanospace depth (460 nm).

Graft linker immobilization for spatial control of protein immobilization inside fused microchips.

Fused silica glass microchips have several attractive features for lab-on-a-chip applications; they can be machined with excellent precision down to nanospace; are stable; transparent and can be modified with a range of silanization agents to change channel surface properties. For immobilization, however, ligands must be added after bonding, since the harsh bonding conditions using heat or hydrofluoric acid would remove all prior immobilized ligands. For spatial control over immobilization, UV-mediated immobilization offers several advantages; spots can be created in parallel, the feature size can be made small, and spatial control over patterns and positions is excellent. However, UV sensitive groups are often based on hydrophobic chemical moieties, which unfortunately result in greater non-specific binding of biomolecules, especially proteins. Here, we present techniques in which any -CH(x) (x=1,2,3) containing surface coating can be used as foundation for grafting a hydrophilic linker with a chemical anchor, a carboxyl group, to which proteins and amine containing molecules can be covalently coupled. Hence, the attractive features of many well-known protein and biomolecule repelling polymer coatings can be utilized while achieving site-specific immobilization only to pre-determined areas within the bonded microchips.

Combining microchip and cell technology for creation of novel biodevices.

Microchip technology has matured over the years into an important field in which novel technologies are being constantly invented, and down-sizing and incorporation of already existing methodologies into the microscale is increasing assay performance and bearing the promise of future total integration for simple, widespread use. One rapidly growing sub-discipline of the microchip research field is focused around the integration of microchip technology and cell biology. In this review, we recapitulate progress here at the Kitamori laboratory in direct relation to cell and microchip technologies, and show some examples of successful integration of the two, going from controlled patterning of cells, on-chip cell culture stimulation, and cardiovascular systems on a chip, to bio-microdevices integrating cardiovascular cells and microtechnology to create novel biodevices such as biocompatible, miniature pumps.