Morphology of 15-mer duplexes tethered to Au(111) probed using scanning probe microscopy

The long-range film structure of 15 base pair, thiol-derivatized duplexes tethered through single 3' and 5' linkages to a Au(111) surface is measured via scanning probe microscopy. Film morphology of the 3' linked duplexes differs from that of its 5' counterpart as observed by scanning probe microscopy in contact mode under buffer solution. No structural features are distinguished in a film formed with the 5' linked duplexes as measured with either a bare silicon nitride or chemically modified probe. However, a distinct pattern in the film structure of the 3' linked duplexes is measured with a chemically modified, hydrophobic tip. Small changes in linker orientation can greatly affect DNA film structure, and a hypothesis for the self-assembly mechanism of the 3' linked duplexes is presented. Factors such as linker placement and composition must be considered in comparing DNA microarrays formed with different tethering methods.