(681c) Molecular Interactions In DNA Surface Hybridization

Solid-phase hybridization underpins modern microarray and biosensor technologies. While the underlying molecular process, namely sequence-specific recognition between complementary probe and target molecules, is fairly well-understood in bulk solution, this knowledge proves insufficient to adequately understand solid-phase hybridization. Using self-assembled DNA "probe" monolayers as a model system, hybridization of probe to target strands is systematically investigated and interpreted. We find that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. The electrostatic barrier to hybridization is studied experimentally through open circuit potential measurements and interpreted using a solution lattice theory model. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes that compete with hybridization to analyte strands. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites.