Mapping of surface-immobilized DNA with force-based atomic force microscopy.

Single-stranded 50-mer, 100-mer, and 150-mer DNAs were immobilized on a surface, and force-based atomic force microscopy (AFM) was employed to examine their behavior. A complementary 20-mer probe DNA on an AFM tip was used for the measurements. High-resolution maps were generated, and relevant parameters, including the force, stretching distance, unbinding probability, cluster size, and degree of distortion, were analyzed. Due to thermal drift, the cluster shape became increasingly distorted as the scan speed was decreased and as the map area was reduced. The cluster radius increased with the number of base (N), and the radius was proportional to N(0.6) (r = 0.977) and N(0.53) (r = 0.991). Due to the effect of the pulling angle, the apparent values of the stretching distance and the unbinding force decreased as the AFM probe was moved away from the center position; these values can be described as a function of sin θ.

Solid phase DNA extraction with a flexible bead-packed microfluidic device to detect methicillin-resistant Staphylococcus aureus in nasal swabs.

We have developed a bead-packed microfluidic device with a built-in flexible wall to automate extraction of nucleic acids from methicillin-resistant Staphylococcus aureus (MRSA) in nasal swabs. The flexible polydimethylsiloxane (PDMS) membrane was designed to manipulate the surface-to-volume ratio (SVR) of bead-packed chambers in the range of 0.05 to 0.15 (µm(-1)) for a typical solid phase extraction protocol composed of binding, washing, and eluting. In particular, the pneumatically assisted close packing of beads led to an invariant SVR (0.15 µm(-1)) even with different bead amounts (10-16 mg), which allowed for consistent operation of the device and improved capture efficiency for bacteria cells. Furthermore, vigorous mixing by asynchronous membrane vibration enabled ca. 90% DNA recovery with ca. 10 µL of liquid solution from the captured cells on the bead surfaces. The full processes to detect MRSA in nasal swabs, i.e., nasal swab collection, prefiltration, on-chip DNA extraction, and real-time polymerase chain reaction (PCR) amplification, were successfully constructed and carried out to validate the capability to detect MRSA in nasal swab samples. This flexible microdevice provided an excellent analytical PCR detection sensitivity of ca. 61 CFU/swab with 95% confidence interval, which turned out to be higher than or similar to that of the commercial DNA-based MRSA detection techniques. This excellent performance would be attributed to the capability of the flexible bead-packed microdevice to enrich the analyte from a large initial sample (e.g., 1 mL) into a microscale volume of eluate (e.g., 10 µL). The proposed microdevice will find many applications as a solid phase extraction method toward various sample-to-answer systems.

Miniaturized bead-beating device to automate full DNA sample preparation processes for gram-positive bacteria.

We have developed a miniaturized bead-beating device to automate nucleic acids extraction from Gram-positive bacteria for molecular diagnostics. The microfluidic device was fabricated by sandwiching a monolithic flexible polydimethylsiloxane (PDMS) membrane between two glass wafers (i.e., glass-PDMS-glass), which acted as an actuator for bead collision via its pneumatic vibration without additional lysis equipment. The Gram-positive bacteria, S. aureus and methicillin-resistant S. aureus, were captured on surface-modified glass beads from 1 mL of initial sample solution and in situ lyzed by bead-beating operation. Then, 10 µL or 20 µL of bacterial DNA solution was eluted and amplified successfully by real-time PCR. It was found that liquid volume fraction played a crucial role in determining the cell lysis efficiency in a confined chamber by facilitating membrane deflection and bead motion. The miniaturized bead-beating operation disrupted most of S. aureus within 3 min, which turned out to be as efficient as the conventional benchtop vortexing machine or the enzyme-based lysis technique. The effective cell concentration was significantly enhanced with the reduction of initial sample volume by 50 or 100 times. Combination of such analyte enrichment and in situ bead-beating lysis provided an excellent PCR detection sensitivity amounting to ca. 46 CFU even for the Gram-positive bacteria. The proposed bead-beating microdevice is potentially useful as a nucleic acid extraction method toward a PCR-based sample-to-answer system.

"Seeing and counting" individual antigens captured on a microarrayed spot with force-based atomic force microscopy.

The mapping capability of atomic force microscopy (AFM) enabled us to see captured prostate-specific antigens (PSAs) on a spot microarrayed with the corresponding antibody and count the number of the antigens in a submicrometer area. To enhance the reliability and the reproducibility of the approach, a third-generation dendron was employed for the surface treatment. The specific force between the captured PSA and the detection antibody (5A6) was measured after cross-linking, and the mean unbinding force was 56 +/- 2 pN. At 100 fM, there were 12 captured antigens in 4.32 x 10(4) nm(2), and the number was dependent upon the concentration. A larger hydrodynamic distance (8 +/- 2 nm) of the immunocomplex resulted in a cluster of pixels corresponding to the single complex in a map recorded over a selected area with a positional interval of 3 nm, and this feature helped to discriminate between pixels of the specific interaction and the nonspecific ones. The results indicate that the approach can be applicable to the quantitative analysis of the antigen in a sample and imply that it can be extended to a sample of very low copy numbers as long as the size of the microarrayed spot is reduced.

Label-free detection of DNA molecules on the dendron based self-assembled monolayer by electrochemical impedance spectroscopy.

We report preparation of a novel platform for effective DNA hybridization and its application to the detection of single mismatched DNA. Cone-shaped dendrimer molecules have been immobilized on the gold surface at equidistance, 3.1 nm, from each other with a probe DNA molecule attached to the top of each dendrimer so that enough space would be secured for effective hybridization. This arrangement allows each probe DNA molecule to form a natural DNA double helix upon hybridization with a target DNA molecule. The single nucleotide polymorphism at either the central or end position of the 25-mer target DNA has been shown to be effectively discriminated against on this platform from each other as well as from a complementary DNA by electrochemical impedance measurements. We also report adverse effects exerted by probe ions, Fe(CN)(6)(3-/4-), on DNA hybridization reactions. The significance of the results for the use in DNA analysis is discussed.

DNA-DNA interaction on dendron-functionalized sol-gel silica films followed with surface plasmon fluorescence spectroscopy.

Since we observed that dendron-assembled surface provided high single nucleotide polymorphism discrimination efficiency for DNA microarrays, and that the binding yield for streptavidin increased when biotin was immobilized on top of it, the nanoscale-controlled surface is examined for surface plasmon field-enhanced fluorescence spectroscopy (or SPFS). Firstly, a silica film was coated onto a gold substrate using the sol-gel technique, followed by the covalent immobilization of a layer of second-generation dendrons with a DNA catcher strand at their apex. The thickness of the inorganic interlayer (d=33 nm) was effectively suppressing fluorescence quenching. Thus, the kinetics and affinity characteristics of DNA hybridization could be investigated very sensitively by SPFS. The kinetic rate constants found for DNA hybridization on the dendron-modified surface were larger than those reported for a streptavidin-modified surface by one order of magnitude, except for dissociation rate constant for a single mismatched case. In addition, we observed that the DNA on the cone-shaped linker maintained its capability to capture DNA target strands even after extended storage at ambient conditions.

Nanoscale-controlled spacing provides DNA microarrays with the SNP discrimination efficiency in solution phase.

We have prepared solid substrates modified with a cone-shaped dendron that generates mesospacing (3.2 nm on average) on the surface. This nanoscale-controlled surface provided an ideal DNA microarray in which each probe DNA strand was given ample space for the incoming target DNA, resulting in selectivity as high as that in solution (100: < 1). In addition, high hybridization yield confirms that DNA probes on the mesospaced surface are sterically unhindered for the hybridization.