DNA condensation has received much attention as a prerequisite for the transport of gene delivery vectors in living cells. Electrophoresis assay is a common method to investigate the interaction between DNA and gene delivery vectors during the DNA condensation process. In order to probe the relation between DNA condensation status and the corresponding electrophoresis behaviour, we synthesized a series of pseudopolyrotaxanes (PPRs) by threading 6-[(6-aminohexyl)amino]-6-deoxy-beta-CD dichloride on the polypropylene glycol and investigated their DNA condensation efficiency by electrophoresis assay. The PPRs of the middle length exhibited the best DNA condensation efficiency in electrophoresis assay, while the shorter or the longer homologues exhibited only slight DNA condensation efficiency. To explain this phenomenon, we investigated the hydrodynamic diameter, the particle size, the zeta potential and the binding affinity of these PPRs/DNA complexes. We found that the stability of PPRs/DNA complexes played an important role in determining the electrophoresis behaviour. Based on the data, we also pointed out the deficiency of electrophoresis assay in investigating the DNA condensation process. Our findings are helpful for researchers engaged in DNA condensation study.