State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China.
Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.
Chembiochem. 2018 Jul 4;19(13):1379-1385. doi: 10.1002/cbic.201800122. Epub 2018 May 30.
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主要是从使用线性单链 (ss) DNA 作为源材料中学到的。例如，用于组装 2D 晶格的典型 DAO（双交叉、反平行、奇数半转）瓷砖的核心结构仅由两条线性 ss-寡核苷酸支架链构建而成，类似于两条绳子打成一个方结。在此，报道了一种新型的偶联 DAO (cDAO) 瓷砖和小圆形 ss-寡核苷酸作为支架链和线性 ss-寡核苷酸作为订书钉链的 2D 晶格。cDAO-c64nt (c64nt：圆形 64 个核苷酸) 的 cDAO 瓷砖，形状为实心平行四边形，在中心有一个 Holliday 连接 (HJ)，在 c64nt 的两个极处有两个 HJ；类似地，cDAO-c84nt，形状为由两个全等三角形组成的交叉四边形，在 c84nt 的中心有一个 HJ 和四个三向连接。从 cDAO 瓷砖组装出完美的 2D 晶格：纳米带、纳米管和纳米环的无限纳米结构以及有限的纳米结构。通过 AFM 成像的可见晶格与相应的看不见的 HJ 二级和三级分子结构、氢键对双螺旋轴的倾斜角度以及瓷砖的手性之间的结构关系可以很好地解释。这项工作为具有独特圆形瓷砖的 DNA 纳米技术提供了新的视角。
