On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

• We apply magnetoresistive sensors to study solid-surface hybridization kinetics of DNA.
• We measure DNA melting profiles for perfectly matching DNA duplexes and for a single base mismatch.
• We present a procedure to correct for temperature dependencies of the sensor output.
• We reliably extract melting temperatures for the DNA hybrids.
• We demonstrate direct measurement of differential binding signal for two probes on a single sensor.

We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches of the differential sensor geometry. The sensor surfaces are functionalized with wild type (WT) and mutant type (MT) capture probes, differing by a single base insertion (a single nucleotide polymorphism, SNP). Complementary biotinylated targets in suspension couple streptavidin magnetic beads to the sensor surface. The beads are magnetized by the field arising from the bias current passed through the sensors. We demonstrate the first on-chip measurements of the melting of DNA hybrids upon a ramping of the temperature. This overcomes the limitation of using a single washing condition at constant temperature. Moreover, we demonstrate that a single sensor bridge can be used to genotype a SNP.