Evaluation of restriction and Cas endonuclease kinetics using matrix-insensitive magnetic biosensors

Denaturation methods for reusable magnetic biosensors

Nanoscale biosensors for sensitive DNA detection require advanced and precise fabrication techniques, which make them highly expensive and result in low yield rates. For such DNA biosensors, sensor regeneration is highly desirable. In this study, we investigated the effectiveness of various denaturants, including ultrapure water, urea solution, tris-ethylenediaminetetraacetic acid buffer, and dimethyl sulfoxide (DMSO), for the denaturation of target DNAs hybridized to probe DNAs on sensors. We used giant magnetoresistive (GMR) biosensors equipped with a temperature control unit in conjunction with magnetic nanoparticles. To examine the effect of DNA sequence on denaturation efficiency, 14 orthogonal DNA pairs were designed and tested. Furthermore, to maintain a consistent sensitivity in subsequent measurements, we evaluated the integrity of the probe DNAs on the sensors after denaturation. Among all the denaturants tested, 40% DMSO demonstrated excellent performance in the denaturation of probe DNAs covalently bonded to the sensors, without any heating process. This optimal denaturant can be applied to other planar DNA biosensor systems; moreover, GMR biosensors can facilitate the evaluation of newly developed denaturants.

Design and Validation of Specific Oligonucleotide Probes on Planar Magnetic Biosensors

Planar DNA biosensors employ surface-tethered oligonucleotide probes to capture target molecules for diagnostic applications. To improve the sensitivity and specificity of biosensing, hybridization affinities should be enhanced, and cross-hybridization with off-targets must be minimized. To this end, assays can be designed using the thermodynamic properties of hybridization between probes and on-targets or off-targets based on Gibbs free energies and melting temperatures. However, the nature of heterogeneous hybridization between the probes on the surface and the targets in a solution imposes challenges in predicting precise hybridization affinities and the degree of cross-hybridization due to indeterminable thermodynamic penalties induced by the solid surface and its status. Herein, we suggest practical and convenient guidelines for designing oligonucleotide probes based on data obtained from planar magnetic biosensors and thermodynamic properties calculated by using easily accessible solution-phase prediction. The suggested requirements comprised Gibbs free energy ≥ -7.5 kcal mol-1 and melting temperature ≤10 °C below the hybridization temperature, and we validated for the absence of cross-hybridization. Additionally, the effects of secondary structures such as hairpins and homodimers were investigated for better oligonucleotide probe designs. We believe that these practical guidelines will assist researchers in developing planar magnetic biosensors with high sensitivity and specificity for the detection of new targets.

Detection of factor Xa activity using giant magnetoresistive biosensors

BACKGROUND

As anticoagulants are widely used to treat patients with atrial fibrillation (AF) and other thrombotic conditions, it is necessary for physicians to determine whether the medication has been taken in emergencies. Among many anticoagulants, rivaroxaban has attracted attention due to its safety and convenience. Since rivaroxaban inhibits activated coagulation factor X (factor Xa), measuring factor Xa activity can determine the presence of rivaroxaban.

RESULTS

We report a magnetic biosensing platform capable of measuring the activity of factor Xa using peptide substrates conjugated with magnetic nanoparticles (MNPs). Due to the size of factor Xa, a new method of solution-phase assays was proposed for magnetic biosensing platforms to address issues with immobilized peptides on the sensors. This method was validated with factor Xa and trypsin, both of which are serine proteases. In the solution-phase assays, samples with either the enzymes of interest or no enzyme were simultaneously measured, and the activity of the enzyme was estimated using the difference between the measurements. Unlike conventional optical methods, our platform was capable of detecting the activity of factor Xa at 2 μg mL-1 with a 30 min sample incubation.

SIGNIFICANCE

The assay using giant magnetoresistive biosensors outperformed conventional optical techniques. This platform can facilitate the determination of the presence of rivaroxaban and assist physicians in deciding on appropriate treatments for patients.