Self-Assembled Magnetic Nanoparticle–Graphene Oxide Nanotag for Optomagnetic Detection of DNA

In this work, a two-dimensional self-assembled magnetic nanoparticle–graphene oxide (MNP-GO) nanocomposite is reported for the detection of DNA. Single-stranded DNA (ssDNA) coils, generated through a rolling circle amplification (RCA) reaction triggered by the hybridization of target oligos and padlock probes, have a strong interaction with MNP-GO nanotags through several mechanisms including π–π stacking, hydrogen bonding, van der Waals, electrostatic, and hydrophobic interactions. This interaction leads to a hydrodynamic size increase or aggregation of MNP-GO nanotags, which can be detected by a simple optomagnetic setup. Due to the high shape anisotropy, MNP-GO nanotags provide stronger optomagnetic signal than individual MNPs. Moreover, the avoidance of DNA probes (i.e., short ssDNA sequences as the biosensing receptor) provides easier material preparation and lower measurement cost. From real-time measurements of interactions between MNP-GO and RCA products amplified from a highly conserved Escherichia coli 16S rDNA sequence, a limit of detection of 2 pM was achieved with a total assay time of 90 min. Although the nonspecific binding force between GO and ssDNA is much weaker than the specific base-pairing force in a DNA duplex, the proposed method provides a detection limit similar to DNA probe-based magnetic biosensors, which can be ascribed to the abundant binding sites between GO and ssDNA. In addition, for target concentrations higher than 100 pM, the MNP-GO nanotags can be applied for a qualitative naked eye detection strategy based on nanotag–ssDNA flocculation.