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

Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-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 ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-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, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-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 double-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.

DNA纳米技术的设计规则大多是从使用线性单链（ss）DNA作为原材料中学到的。例如，用于组装二维晶格的典型DAO（双交叉、反平行、奇数半圈）瓦片的核心结构仅由两条线性单链寡核苷酸支架链构建而成，类似于两条绳子打一个平结。在此，报道了一种新型的耦合DAO（cDAO）瓦片以及以小的环形单链寡核苷酸作为支架链和线性单链寡核苷酸作为 staple链的二维晶格。cDAO - c64nt（c64nt：环形64个核苷酸）的cDAO瓦片形状为实心平行四边形，由在一个c64nt的中心有一个霍利迪连接点（HJ）以及在两极各有一个HJ构成；类似地，cDAO - c84nt形状为由两个全等三角形组成的交叉四边形，由在一个c84nt的中心有一个HJ以及在角上有四个三路连接点形成。由cDAO瓦片组装出了完美的二维晶格：纳米带、纳米管和纳米环的无限纳米结构以及有限纳米结构。原子力显微镜成像的可见晶格与相应的不可见的HJ二级和三级分子结构、氢键相对于双螺旋轴的倾斜角以及瓦片的手性之间的结构关系可以得到很好的解释。这项工作可能会为具有独特环形瓦片的DNA纳米技术带来新的启示。