Kenji Arinaga

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 × 108 bound targets per cm2 sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

Electrical manipulation of oligonucleotides grafted to charged surfaces

The electrical manipulation of short DNA molecules on surfaces offers novel functionalities with fascinating possibilities in the field of bio-interfaces. Here we present systematic investigations of the electrical interactions which govern the structure of oligonucleotides on charged gold surfaces. Successively, we address influences of the applied field strength, the role of DC electrode potentials, in particular for polycrystalline surfaces, as well as screening effects of the surrounding electrolyte solution. Data obtained for single and double stranded DNA exhibit differences which can be attributed to the dissimilar flexibility of the different molecular conformations. A comparison of the experimental results with a basic model shows how the alignment of the molecules adjusts according to a balance between electrically induced ordering and stochastic thermal motions. The presented conclusions are expected to be of general relevance for the behaviour of polyelectrolytes exposed to localized electric fields at interfaces.

Detection and Size Analysis of Proteins with Switchable DNA Layers

We introduce a chip-compatible scheme for the label-free detection of proteins in real-time that is based on the electrically driven conformation switching of DNA oligonucleotides on metal surfaces. The switching behavior is a sensitive indicator for the specific recognition of IgG antibodies and antibody fragments, which can be detected in quantities of less than 10(-18) mol on the sensor surface. Moreover, we show how the dynamics of the induced molecular motion can be monitored by measuring the high-frequency switching response. When proteins bind to the layer, the increase in hydrodynamic drag slows the switching dynamics, which allows us to determine the size of the captured proteins. We demonstrate the identification of different antibody fragments by means of their kinetic fingerprint. The switchDNA method represents a generic approach to simultaneously detect and size target molecules using a single analytical platform.

Excessive Counterion Condensation on Immobilized ssDNA in Solutions of High Ionic Strength

We present experiments on the bias-induced release of immobilized, single-stranded (ss) 24-mer oligonucleotides from Au-surfaces into electrolyte solutions of varying ionic strength. Desorption is evidenced by fluorescence measurements of dye-labeled ssDNA. Electrostatic interactions between adsorbed ssDNA and the Au-surface are investigated with respect to 1), a variation of the bias potential applied to the Au-electrode; and 2), the screening effect of the electrolyte solution. For the latter, the concentration of monovalent salt in solution is varied from 3 to 1600 mM. We find that the strength of electric interaction is predominantly determined by the effective charge of the ssDNA itself and that the release of DNA mainly occurs before the electrochemical double layer has been established at the electrolyte/Au interface. In agreement with Mannings condensation theory, the measured desorption efficiency (etarel) stays constant over a wide range of salt concentrations; however, as the Debye length is reduced below a value comparable to the axial charge spacing of the DNA, etarel decreases substantially. We assign this effect to excessive counterion condensation on the DNA in solutions of high ionic strength. In addition, the relative translational diffusion coefficient of ssDNA in solution is evaluated for different salt concentrations.

A silicon-on-insulator vertical nanogap device for electrical transport measurements in aqueous electrolyte solution

A novel concept for metal electrodes with few 10 nm separation for electrical conductance measurements in an aqueous electrolyte environment is presented. Silicon-on-insulator (SOI) material with 10 nm buried silicon dioxide serves as a base substrate for the formation of SOI plateau structures which, after recess-etching the thin oxide layer, thermal oxidation and subsequent metal thin film evaporation, feature vertically oriented nanogap electrodes at their exposed sidewalls. During fabrication only standard silicon process technology without any high-resolution nanolithographic techniques is employed. The vertical concept allows an array-like parallel processing of many individual devices on the same substrate chip. As analysed by cross-sectional TEM analysis the devices exhibit a well-defined material layer architecture, determined by the chosen material thicknesses and process parameters. To investigate the device in aqueous solution, we passivated the sample surface by a polymer layer, leaving a micrometre-size fluid access window to the nanogap region only. First current–voltage characteristics of a 65 nm gap device measured in 60 mM buffer solution reveal excellent electrical isolation behaviour which suggests applications in the field of biomolecular electronics in a natural environment.

Microfluidic biosensor for the detection of DNA by fluorescence enhancement and the following streptavidin detection by fluorescence quenching.

We reported an optical DNA/protein microfluidic sensor which consists of single stranded (ss) DNA-Cy3 probes on gold surface and simple line-shape microfluidic channel. These ssDNA-Cy3 probes with random sequence in bulk solution or on gold surface exhibits fluorescence enhancement after binding with complementary ssDNA (cssDNA) targets. Particularly it did not require complicated design or hairpin-like stem-loop conformation, which made it easier to be made and applied in analytes detection by fluorescence switching techniques. Using ssDNA-cy3 probes attached on gold surface in a microfluidic channel, strong fluorescence enhancement was measured by ssDNA with cssDNA binding or ssDNA with cssDNA-biotin binding. The following introduction of streptavidin resulted in fluorescence quenching (fluorescence decrease) because of the binding of hybridized DNA-biotin with streptavidin. This sensor showed strong affinity and high sensitivity toward the streptavidin, the minimum detectable concentration for streptavidin was 1 pM, equating to an absolute detection limit of 60 amol in this microfluidic channel. Microfluidic channel height and flow rate is optimized to increase surface reaction efficiency and fluorescence switching efficiency. In contrast to previously reported optical molecular beacon approach, this sensor can be used not only for the detection of cssDNA target, but also for the detection of streptavidin. This microfluidic sensor offers the promise of analyzing kinds of molecular targets or immunoreactions.

A deep microfluidic absorbance detection cell replicated from a thickly stacked SU-8 dry film resist mold

Dry film resist SU-8 was used to make a thick mold for soft lithography of a poly(dimethylsiloxane) (PDMS) microfluidic chip with deep channels. The stacking of the SU-8 film enabled an ultra-thick (up to 500 μm) resist process on Si wafer. This process was fast and highly reproducible compared with the conventional liquid SU-8 process. The deep channel in the PDMS chip was utilized as a micro-flow cell for sensitive absorbance measurement. Sunset Yellow FCF dye was used to demonstrate absorption spectroscopy in the deep channel. Since the channel depth was proportional to the optical path length, which was proportional to the absorbance value, the PDMS chip achieved a detection limit (15.9 μM) comparable to U- or Z-shaped microfabricated absorbance detection cells in glass. Calibration curves for different solution concentrations were obtained with good R2 values (∼1).

Evaluation of HgCdTe using laser beam induced current

We have developed a nondestructive evaluation method for HgCdTe. We focused on laser beam induced current (LBIC) which features a high specific resolution and nondestructive evaluation. The LBIC technique shows the electrically active regions in HgCdTe wafer as an image. We have considered the measurement temperature versus the LBIC signal. The LBIC technique at room temperature (300 K) can be used to evaluate non-uniformities in carrier concentrations in HgCdTe more sensitively. Using etch pit studies and secondary ion mass spectroscopy (SIMS), we have identified that non-uniformities of carrier concentration in the HgCdTe wafer arise from metal impurities around dislocation clusters. This nondestructive technique is useful for screening HgCdTe wafers before fabricating devices.

Electrical Manipulation of DNA on Metal Surfaces

We review recent work on the active manipulation of DNA on metal substrates by electric fields. This includes the controlled positioning, alignment, or release of DNA on or into dedicated locations and the control of hybridization. In this context, we discuss techniques for immobilizing DNA on metal surfaces and methods of characterizing such hybrid systems. In particular, we focus on electrically induced, conformational changes of monolayers of short oligonucleotides on gold substrates. Such switchable layers allow for molecular dynamics studies at interfaces and have demonstrated large potential in label-free biosensing applications.

CdTe films deposited by helicon sputtering for p-type Hg0.77Cd0.23Te surface passivation

We investigated the passivation properties of CdTe films that were deposited on p-type Hg0.77Cd0.23Te using the helicon sputtering method. Crystallinity and morphological microstructure of the CdTe films were determined by transmission electron microcopy and atomic force microscopy, respectively. We found that the CdTe films are polycrystalline and provide good morphological properties: they have no granular-type defects and no pin-holes. Electrical measurements of metal-insulator semiconductor devices showed that the properties of the CdTe/HgCdTe interface mainly depend on deposition pressure and the conditions of post-deposition annealings. It was observed that CdTe deposition at higher pressure reduces the surface deposition damage that is responsible for increasing the positive fixed charges, the slow traps and other degradations of the HgCdTe surface. Moreover, post-deposition annealing at a temperature above 100 degrees Celsius improves the thermal stability of the electrical properties of the interface. A gate-controlled diode that was produced with post-deposition annealing showed that CdTe films deposited by helicon sputtering were essentially suitable for passivation of HgCdTe photodiode arrays.