Perylene diimide (PDI)-oligonucleotide conjugates can form either duplex or hairpin dimer structures, depending upon the choice of oligonucleotide base sequence. PDI dimer formation occurs either upon hybridization of complementary strands in which PDI is located at mid-strand or upon association of PDI-linked hairpins to form hairpin dimers. A combination of molecular modeling and circular dichroism spectroscopy reveals that the geometry of the PDI dimer is different in these systems, having a non-parallel and parallel structures in the duplex and hairpin dimer, respectively. Addition of poly-T oligomers to the hairpin dimer results in the formation of remarkably stable triplex structures in which the hairpin/oligomer stoichiometry is determined by the length of the oligomer. Capped hairpin and dumbbell structures possessing PDI at both ends form linear oligomers assembled by head-to-head or head-to-tail PDI dimer formation. Femtosecond pump-probe spectroscopy has revealed that the dynamics of charge separation and charge recombination are dependent upon the structure of the assembly.