Assembly of dsDNA nanocircles into dimeric and oligomeric aggregatesw

Nucleic acids are an ideal material for the construction of nanometre-scaled objects. DNA-based scaffolds of different topological and mechanical properties have been generated and applications for ordered nucleic acid nanoarchitectures have been implemented. Nucleic acids have also been used for building devices like walkers, tweezers, thermometers, or self-replicating systems, and for the directed conjugation of biomaterials. In programming the assembly of higher-order nanoparticle structures in which DNA is used as a mould, supramolecular principles that go beyond the classical Watson–Crick-based association of DNA-strands have been harnessed. Among them, the hybridization of chemically functionalized ODNs with metal-chelating groups, intercalators, nanoparticles, or externally added molecular struts has proven useful. We have previously described the efficient synthesis of dsDNA minicircles containing bespoke single-stranded (ss) gap regions. These dsDNA-circles hardly exhibit any ring strain because they contain repetitive, intrinsically bent AT-tracts that cooperatively result in a circular shape of the double helix with 105, 126, 147, 168, or more base-pairs (bp). The ss-gaps can be used as handles for functionalizing the dsDNA-rings. We have established a new type of mixed DNA architectures, where RNA-aptamer motifs or polypeptide struts directed the assembly of circular dsDNA nanoobjects into higher order architectures in a precisely defined fashion. The ss-gap also allowed the introduction of chemical groups into a dsDNA nanoring. For example, we synthesized anthracene-modified ODNs containing one, two, or more anthracene residues in a single 21-mer ODN that is complementary to the gap. Hybridizing these ODNs to the ss gap region provided access to dsDNA nanocircles containing anthracene modifications at defined positions. The anthracene groups were attached to C5 of deoxyuridyl residues via a flexible linker in a way that the intercalator protrudes from the helix by a length of approximately 10 Å (Fig. 1). This length is sufficient for the aromatic residue to intercalate into a neighbouring dsDNA nanocircle, but is short enough to prevent self-intercalation. Such a mode of interaction could be cooperative in a way that either results in a combination of nanocircles at their sites of functionalization, which would lead to the assembly of two nanocircles, or, alternatively, could be omnidirectional, leading to oligomeric aggregation of multiple nanocircles. Here we have addressed this issue by analysing the selfassembly of anthracene-containing dsDNA nanocircles by atomic force microscopy (AFM). dsDNA nanocircles are well