Flexibility of C sub(3h)-Symmetrical Linkers in Tris-oligonucleotide-Based Tetrahedral Scaffolds

Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C sub(3)h-symmet rical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established. Tweaking tiny tetrahedrons: Tris-oligonucleotide flexibility is determined by hydrocarbon chains at the linker core, which allow a set of four tris-oligonucleotides to fold into a tetrahedral nanocage. So far, the feasibility of methylene and ethylene chains is unexplored. A new generation of isocyanurate-based linkers was developed to offer easier and facile access to tris-oligonucleotides.