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‐olig...

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Bibliographic Details
Published in:Chembiochem : a European journal of chemical biology 2018-07, Vol.19 (13), p.1379-1385
Main Authors: Guo, Xin, Wang, Xue‐Mei, Wei, Shuai, Xiao, Shou‐Jun
Format: Article
Language:English
Subjects:
Chirality
Circular DNA
Circularity
Construction
Deoxyribonucleic acid
Dimensional stability
DNA
DNA structures
Hydrogen bonding
Hydrogen bonds
Inclination angle
Lattices
Molecular chains
Nanostructure
Nanotechnology
Nanotubes
noncovalent interactions
Nucleotides
Oligonucleotides
Scaffolds
self-assembly
Strands
structure elucidation
Tiles
Triangles
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Summary: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. 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.
ISSN:1439-4227
1439-7633
DOI:10.1002/cbic.201800122