Monday, June 16, 2008 - 10:55 AM
Room 6 (McKimmon Conference Center)
48

Hybrid Bilayers Hosting PNA Surfactants: DNA Binding Kinetics, Selectivity, and Surface Mobility

James W. Schneider and Travis Crites. Carnegie Mellon University, Pittsburgh, PA

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.