Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Twoâ Dimensional Lattices

Abstract

Design rules for DNA nanotechnology have been mostly learnt from using linear singleâ stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd halfâ turns) tile for assembling 2D lattices is constructed from only two linear ssâ oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ssâ oligonucleotides as scaffold strands and linear ssâ oligonucleotides as staple strands are reported. A cDAO tile of cDAOâ c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAOâ c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four threeâ way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the doubleâ helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.Bending the rules: The design of DNA motifs and lattices has mostly been investigated by using linear singleâ stranded DNA molecules as source materials. New coupled DAO (double crossover, antiparallel, odd halfâ turns) motifs and lattices have been constructed from small circular DNA molecules as scaffolds.