Antiparallel DNA Double Crossover Molecules As Components for Nanoconstruction

TLDR

Double crossover DNA molecules consist of two Holliday junctions linked by two helical arms, and they exist in parallel or antiparallel orientations with varying half‑turn counts between crossovers. The study investigates the suitability of antiparallel double‑crossover DNA molecules for use in nanoconstruction. The authors characterized antiparallel DAE molecules by ligation‑cyclization assays, comparing a conventional DAE with a bulged three‑arm variant. The antiparallel DAE molecules cyclize poorly, showing no advantage over a linear control, and while the conventional variant is slightly stiffer, the scarcity of cyclic products limits comparison; nevertheless, they may serve as rigid elements for building symmetric lattices and could be paired with DNA triangles and deltahedra.

Abstract

Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. We have examined these molecules from the viewpoint of their potential utility in nanoconstruction. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, so these have been characterized in a ligation cyclization assay. In contrast to other molecules that contain branched junctions, we find that these molecules cyclize rarely or not at all. The double crossover molecules cyclize no more readily than the linear molecule containing the same sequence as the ligation domain. We have tested both a conventional DAE molecule and one containing a bulged three-arm branched junction between the crossovers. The conventional DAE molecule appears to be slightly stiffer, but so few cyclic products are obtained in either case that quantitative comparisons are not possible. Thus, it appears that these molecules may be able to serve as the rigid components that are needed to assemble symmetric molecular structures, such as periodic lattices. We suggest that they be combined with DNA triangles and deltahedra in order to accomplish this goal.