Controlled Reassociation of Multistranded, Polycrossover DNA Molecules into Double Helices

Shape-changing DNA nanostructures have found applications in biosensing, drug delivery, and data storage. Here, we use sequence and temperature-controlled reassociation of one type of a DNA nanostructure (paranemic crossover (PX) DNA) into another structure (duplex). 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 demonstrate tunable biostability, where the structures before and after reassociation show vastly different nuclease resistance against DNase I. We further extend the strategy to other polycrossover DNA molecules such as a double crossover motif and a juxtaposed DNA motif, 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 DNA-based materials and devices.