Discrete Au nanoparticle/DNA conjugates have been isolated by electrophoresis and used to form small groupings of particles, such as dimers and trimers. The use of purified conjugates leads to a higher yield of the target structure, and it has allowed us better control and understanding of the system. Newly accessible questions, such as the electrophoretic mobility of nanoparticle/DNA hybrids and the critical role of particle surface charge on mobility, have been studied. Detailed characterization by transmission electron microscopy (TEM) has now been done because of the higher quality of the samples. A computer program to generate pair distribution functions from TEM images was developed, pointing out the dependence of interparticle distance with DNA length on dimers of particles.