Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two‐Dimensional Lattices. (30th May 2018)

• Record Type: Journal Article
• Authors: Guo, Xin; Wang, Xue‐Mei; Wei, Shuai; Xiao, Shou‐Jun
• Is Part Of: Chembiochem. Volume 19:Number 13(2018)
• Page Start: 1379
• Page End: 1385
• Publication Date: 2018-05-30
• Subjects: DNA structures -- nanotechnology -- noncovalent interactions -- self-assembly -- structure elucidation; Biochemistry -- Periodicals; Molecular biology -- Periodicals; Pharmaceutical chemistry -- Periodicals; 572
• DOI: 10.1002/cbic.201800122
• Languages: English
• ISSNs: 1439-4227

Abstract

Abstract: 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. Abstract : Bending the rules : The design of DNA motifs and lattices has mostly been investigated by using linear single‐stranded DNA molecules as source materials. New coupled DAO (double crossover, antiparallel, odd half‐turns) motifs and lattices have been constructed from small circular DNA molecules as scaffolds.