Controlled reassociation of multistranded, polycrossover DNA molecules into double helices

Shape-changing DNA nanostructures have found applications in biosensing, drug delivery, cell modulation and data storage. A key aspect of this reconfiguration is the interaction of DNA nanostructures with other biomolecules or chemical stimuli such as pH and ionic conditions. Sequence-based nanostructure reconfiguration is largely achieved by strand displacement which is based on single stranded toeholds. In this work, we use sequence and temperature-controlled reassociation of one type of a DNA nanostructure into another structure. We demonstrate this strategy using the paranemic crossover (PX) DNA, a four-stranded structure with two adjacent double helical domains connected by six strand crossovers. In the presence of an anti-PX structure that is composed of strands that are each complementary to those in PX DNA, the structures reassociate at specific temperatures to form duplexes. Using the denaturing agent formamide, we decreased the temperature required for this reassociation. We extend the strategy to other polycrossover DNA molecules such as a double crossover motif (2 crossovers) and a juxtaposed DNA motif (4 crossovers), showing controlled reassociation of different DNA motifs into duplexes. Our study highlights the potential for DNA motifs to function as switchable molecular systems, offering new insights for responsive DNA-based materials and devices.