The role of probe-probe interactions on the hybridization of double-stranded DNA targets onto DNA-modified magnetic microparticles

In this work, we have studied the effect of different probe lengths and surface densities on the hybridization of a 181-bp polymerase chain reaction product to probes tethered onto magnetic microparticles. Hybridization was shown to be favored by longer probes but only at probe surface densities where probe-to-probe interactions are absent. From these results, a simple rule was inferred for determining maximum surface densities above which hybridization signals decreased. According to this rule, if the average surface area occupied by an immobilized probe (I ) pound is larger than the projected surface area of each tethered probe molecule (S (ss) ), hybridization efficiency increases with surface density, whereas the reverse occurs when I pound - S (ss) < 0.