Frederik Westergaard Østerberg

Novel Readout Method for Molecular Diagnostic Assays Based on Optical Measurements of Magnetic Nanobead Dynamics

We demonstrate detection of DNA coils formed from a Vibrio cholerae DNA target at picomolar concentrations using a novel optomagnetic approach exploiting the dynamic behavior and optical anisotropy of magnetic nanobead (MNB) assemblies. We establish that the complex second harmonic optical transmission spectra of MNB suspensions measured upon application of a weak uniaxial AC magnetic field correlate well with the rotation dynamics of the individual MNBs. Adding a target analyte to the solution leads to the formation of permanent MNB clusters, namely, to the suppression of the dynamic MNB behavior. We prove that the optical transmission spectra are highly sensitive to the formation of permanent MNB clusters and, thereby to the target analyte concentration. As a specific clinically relevant diagnostic case, we detect DNA coils formed via padlock probe recognition and isothermal rolling circle amplification and benchmark against a commercial equipment. The results demonstrate the fast optomagnetic readout of rolling circle products from bacterial DNA utilizing the dynamic properties of MNBs in a miniaturized and low-cost platform requiring only a transparent window in the chip.

Measurements of Brownian relaxation of magnetic nanobeads using planar Hall effect bridge sensors.

We compare measurements of the Brownian relaxation response of magnetic nanobeads in suspension using planar Hall effect sensors of cross geometry and a newly proposed bridge geometry. We find that the bridge sensor yields six times as large signals as the cross sensor, which results in a more accurate determination of the hydrodynamic size of the magnetic nanobeads. Finally, the bridge sensor has successfully been used to measure the change in dynamic magnetic response when rolling circle amplified DNA molecules are bound to the magnetic nanobeads. The change is validated by measurements performed in a commercial AC susceptometer. The presented bridge sensor is, thus, a promising component in future lab-on-a-chip biosensors for detection of clinically relevant analytes, including bacterial genomic DNA and proteins.

Scalable DNA-Based Magnetic Nanoparticle Agglutination Assay for Bacterial Detection in Patient Samples

We demonstrate a nanoparticle-based assay for the detection of bacteria causing urinary tract infections in patient samples with a total assay time of 4 h. This time is significantly shorter than the current gold standard, plate culture, which can take several days depending on the pathogen. The assay is based on padlock probe recognition followed by two cycles of rolling circle amplification (RCA) to form DNA coils corresponding to the target bacterial DNA. The readout of the RCA products is based on optomagnetic measurements of the specific agglutination of DNA-bound magnetic nanoparticles (MNPs) using low-cost optoelectronic components from Blu-ray drives. We implement a detection approach, which relies on the monomerization of the RCA products, the use of the monomers to link and agglutinate two populations of MNPs functionalized with universal nontarget specific detection probes and on the introduction of a magnetic incubation scheme. This enables multiplex detection of Escherichia coli, Proteus mirabilis and Pseudomonas aeruginosa at clinically relevant concentrations, demonstrating a factor of 30 improvement in sensitivity compared to previous MNP-based detection schemes. Thanks to the universal probes, the same set of functionalized MNPs can be used to read out products from a multitude of RCA targets, making the approach truly scalable for parallel detection of multiple bacteria in a future integrated point of care molecular diagnostics system.

On‐Chip Detection of Rolling Circle Amplified DNA Molecules from Bacillus Globigii Spores and Vibrio Cholerae

For the first time DNA coils formed by rolling circle amplification are quantified on-chip by Brownian relaxation measurements on magnetic nanobeads using a magnetoresistive sensor. No external magnetic fields are required besides the magnetic field arising from the current through the sensor, which makes the setup very compact. Limits of detection down to 500 Bacillus globigii spores and 2 pM of Vibrio cholerae are demonstrated, which are on the same order of magnitude or lower than those achieved previously using a commercial macro-scale AC susceptometer. The chip-based readout is an important step towards the realization of field tests based on rolling circle amplification molecular analyses.

Magnetoresistive sensor for real-time single nucleotide polymorphism genotyping

We demonstrate a magnetoresistive sensor platform that allows for the real-time detection of point mutations in DNA targets. Specifically, we detect point mutations at two sites in the human beta globin gene. For DNA detection, the present sensor technology has a detection limit of about 160 pM and a dynamic range of about two orders of magnitude. The sensors are based on a new geometry for biological sensing that detects the difference between the amount of beads bound to a sensing pad and a local integrated negative reference pad. The magnetic beads are magnetised by the magnetic field arising from the sensor bias current such that no external magnetic fields are needed. The sensors are integrated in a microfluidic system with temperature control. The local negative reference integrated in the sensor geometry efficiently compensates for sensor offsets, external magnetic fields and a uniform background of magnetic beads, which enables real-time quantification of the specific binding of magnetic beads to the sensor surface under varying experimental conditions.

Bead Capture on Magnetic Sensors in a Microfluidic System

The accumulation of magnetic beads by gravitational sedimentation and magnetic capture on a planar Hall-effect sensor integrated in a microfluidic channel is studied systematically as a function of the bead concentration, the fluid flow rate, and the sensor bias current. It is demonstrated that the sedimentation flux is proportional to the bead concentration and has a power law relation to the fluid flow rate. The mechanisms for the bead accumulation are investigated and it is found that gravitational sedimentation dominates the bead accumulation, whereas the stability of the sedimented beads against the fluid flow is defined by the localized magnetic fields from the sensor.

Planar Hall effect bridge geometries optimized for magnetic bead detection

Novel designs of planar Hall effect bridge sensors optimized for magnetic bead detection are presented and characterized. By constructing the sensor geometries appropriately, the sensors can be tailored to be sensitive to an external magnetic field, the magnetic field due to beads being magnetized by the sensor self-field or a combination thereof. The sensors can be made nominally insensitive to small external magnetic fields, while being maximally sensitive to magnetic beads, magnetized by the sensor self-field. Thus, the sensor designs can be tailored towards specific applications with minimal influence of external variables. Three different sensor designs are analyzed theoretically. To experimentally validate the theoretical signals, two sets of measurements are performed. First, the sensor signals are characterized as function of an externally applied magnetic field. Then, measurements of the dynamic magnetic response of suspensions of magnetic beads with a nominal diameter of 80 nm are performed. Fur...

On-chip measurements of Brownian relaxation of magnetic beads with diameters from 10 nm to 250 nm

We demonstrate the use of planar Hall effect magnetoresistive sensors for AC susceptibility measurements of magnetic beads with frequencies ranging from DC to 1 MHz. This wide frequency range allows for measuring Brownian relaxation of magnetic beads with diameters ranging from 10 nm to 250 nm. Brownian relaxation is measured for six different magnetic bead types and their hydrodynamic diameters are determined. The hydrodynamic diameters are found to be within 40% of the nominal bead diameters. We discuss the applicability of the different bead types for volume-based biosensing with respect to sedimentation, magnetic trapping, and signal per bead. Among the investigated beads, we conclude that the beads with a nominal diameter of 80 nm are best suited for future on-chip volume-based biosensing experiments using planar Hall effect sensors.

Mesoscopic current transport in two-dimensional materials with grain boundaries: Four-point probe resistance and Hall effect

We have studied the behavior of micro four-point probe (M4PP) measurements on two-dimensional (2D) sheets composed of grains of varying size and grain boundary resistivity by Monte Carlo based finite element (FE) modelling. The 2D sheet of the FE model was constructed using Voronoi tessellation to emulate a polycrystalline sheet, and a square sample was cut from the tessellated surface. Four-point resistances and Hall effect signals were calculated for a probe placed in the center of the square sample as a function of grain density n and grain boundary resistivity ρGB. We find that the dual configuration sheet resistance as well as the resistance measured between opposing edges of the square sample have a simple unique dependency on the dimension-less parameter nρGBG0, where G0 is the sheet conductance of a grain. The value of the ratio RA/RB between resistances measured in A- and B-configurations depends on the dimensionality of the current transport (i.e., one- or two-dimensional). At low grain density ...

Fast micro Hall effect measurements on small pads

Sheet resistance, carrier mobility, and sheet carrier density are important parameters in semiconductor production, and it is therefore important to be able to rapidly and accurately measure these parameters even on small samples or pads. The interpretation of four-point probe measurements on small pads is non-trivial. In this paper we discuss how conformal mapping can be used to evaluate theoretically expected measurement values on small pads. Theoretical values calculated from analytical mappings of simple geometries are compared to the values found from the numerical conformal mapping of a square onto the infinite half-plane, where well-established solutions are known. Hall effect measurements are performed to show, experimentally, that it is possible to measure Hall mobility in less than one minute on squares as small as 70 × 70 μm2 with a deviation of ±6.5% on a 1σ level from accurate reference measurements, when only small sheet resistance variations are present. For samples with a sheet resistance ...