Conformation of oligonucleotides attached to gold nanocrystals probed by gel electrophoresis

Thiol-modified single stranded oligonucleotides of different lengths (8 to 135 bases) were attached to the surface of 10 nm diameter Au nanocrystals with different DNA/Au ratios (1, 2,...,saturation). The electrophoretic mobility of these conjugates was determined on 2% agarose gels, and the effective diameter of the DNA/Au conjugates was determined. This diameter depends on the conformation of the oligonucleotides adsorbed on the Au surface. For low surface coverage, nonspecific wrapping of the DNA around the nanoparticles was observed. For high surface coverage, short oligonucleotides were shown to be oriented perpendicular to the surface and fully stretched. For high surface coverage and long oligonucleotides, the inner part close to the Au surface was determined to be fully stretched and pointed perpendicular to the surface, whereas the outer part adopts random coil shape.