(503c) Surface Morpholino-DNA Interaction Study At Different Ionic Strengths

Though powerful, DNA microarray technology is also complicated by the multiplicity of interactions that arise during a hybridization experiment. These interactions include those between nucleic acid strands in solution, between strands immobilized on the microarray surface, and the desired cross-interaction where one member of a hybridizing pair is on the surface and the other in solution. One approach to improved contrast for selecting the interaction of interest against the background of competing interactions is to use a non-DNA probe on the microarray. This study considers a non-ionic probe, morpholino (MO), which is a synthetic nucleic acid analog with an uncharged backbone. Under low ionic strength, the neutral backbone provides improved binding to complementary DNA when compared to DNA-DNA interactions; this feature helps select out the MO-DNA surface hybridization while destabilizing solution interactions (i.e. secondary structure) present in the analyte mixture.

This work develops protocols for preparing and using morpholino microarrays. Commercial aldehyde slides were chosen as the solid support due to their uncharged surface and reported good performance when used with DNA probes. To better understand the hybridization behavior of morpholinos on microarrays, both single-stranded and double-stranded DNA targets were assayed and the observed hybridization trends were interpreted in terms of the molecular organization of the probe films and effects derived from additives in the hybridization cocktail. Phosphate buffers with concentrations from 0 to 1 mol L^-1 were used to reveal the influence of ionic strength. Based on solution melting results, selectivity of MO-DNA hybridization is enhanced as ionic strength decreases. This trend is consistent with surface hybridization results, which reveal that optimal usage conditions for MO-DNA microarrays are at low ionic strengths.