Ligation of Triangles Built from Bulged 3-Arm DNA Branched Junctions

An important stepping stone to controlled construction on the nanometer scale is the development of rigid components, building blocks whose directions of bonding bear fixed angular relationships to each other. We are exploring nanoconstruction with branched DNA junctions. Branched junctions with three and four arms are known to be flexible, but 3-arm branched junctions containing bulges are known to have a preferred stacking direction. Here, we have tested the rigidity of equilateral triangles whose vertices are all bulged 3-arm branched junctions. There are two kinds of equilateral triangles with an integral number of turns per edge that can be made from these components:  those with the bulges on the inside strand, and those with the bulges on the outside strand. Alternating the two species generates a reporter strand. Each triangle is assembled and purified as a topologically closed species. Assembly of the triangle with the bulges on the inner strand results in two topoisomers that can be separated. S...