Label-free DNA microarray bioassays using a near-field scanning microwavemicroscope

A near-field scanning microwave microscope (NSMM) is used to readout and visualize homemade 10-mer oligonucleotide microarrays and an Agilent 60-mer DNA microarray as a realistic test of NSMM applicability to multiplexed sequence analysis. Sensitive characterization of DNA coverage and high resolution mapping of DNA spots in the microarray were realized by measuring the change of microwave reflection coefficient (S11) at about 4 GHz operating frequency. Hybridization between target (free) and capture (immobilized) sequences leads to changes in the microwave reflection coefficient, which were measured by the NSMM. These changes are caused by hybridization-induced modification of the dielectric permittivity profile of the DNA film. The dynamic range based on analysis of the 10-mer microarrays is over 3orders of magnitude with the detection limit estimated below 0.01 strands/μm2. The NSMM method should be readily capable of detecting target coverages down to 98% of probe coverage. We also directly image the patterned DNA microarray by NSMM with a 2 μm resolution. The complementary optical image of the DNA microarray visualized by using a relative fluorescent intensity metric agrees well with the NSMM results.

► We visualized Agilent 60-mer DNA microarray by a NSMM with a 2 μm resolution.
► NSMM should be capable of detecting target coverage down to 98% of probe coverage.
► Hybridization leads to changes in the microwave reflection coefficient S11.
► NSMM could be used to confirm quality of manufacture to flag any defectivespots.