Countless bioanalytical devices, including microarrays, rely on the hybridization of DNA introduced in solution to DNA oligomer probes immobilized on surfaces. The presence of a detecting surface allows sensitive detection methods to be employed, including and laser-induced fluorescence and waveguide-based modalities. Probes can also be located at addressable spots for high-throughput, multiplexed analysis. However, it is now widely appreciated that surface hybridization process can be several orders of magnitude slower than their solution-phase counterparts. This is due primarily to electrostatic and steric penalties imposed by the probe layer as target molecules diffuse toward the surface. We are developing a platform that aims to retain the advantages of surface-based sensing while improving hybridization kinetics. Water-insoluble, di-alkyl surfactants composed of the uncharged nucleic acid analogue PNA (peptide nucleic acid) are suspended in buffer, then hydrated by a series of freeze-thaw cycles. The hydrated suspension is flowed over a C18-silanated silica surface to create a hybrid bilayer (see figure). Measurements using dual-polarization interferometry show that the PNAs adopt a flat conformation under these conditions and have surface densities comparable to immobilized DNA probes. Following introduction of complementary and mismatch DNA targets, PNA-DNA hybridization kinetics are measured using a combined TIRF-FRET method, showing 10-fold or greater improvements in binding kinetics compared to immobilized probes. We will discuss the ability of the hybrid-bilayer system to accommodate overhanging bases of DNA, and the role of surface diffusion processes on the improved kinetics.
