Facile characterization of topology of DNA catenanes

Abstract During the preparation of single-stranded DNA catenanes, topological isomers of different linking numbers (Lk) are intrinsically produced, and they must be separated each other to construct sophisticated nanostructures accurately. In many of previous studies, however, mixtures of these isomers were directly employed to construct nanostructures without sufficient characterization. Here, we present a method which easily and clearly characterizes the isomers by polyacrylamide gel electrophoresis (PAGE). To the mixtures of topological isomers of [2]catenanes, two strut oligonucleotides, which are complementary with a part of both rings, were added to connect the rings and fix the whole conformations of isomers. As a result, the order of migration rate was always Lk3 > Lk2 > Lk1, irrespective of gel concentration. Thus, all the topological isomers were unanimously characterized by only one PAGE experiment. Well-characterized DNA catenanes are obtainable by the present two-strut strategy, opening the way to still more advanced nanotechnology.