2D DNA lattices assembled from DX-coupled tiles

Wei Zhang; Chuan Jiang; Xin Guo; Mirza Muhammad Faran Ashraf Baig; Caihong Ni; Shou-Jun Xiao

doi:10.1016/j.jcis.2022.02.038

2D DNA lattices assembled from DX-coupled tiles

J Colloid Interface Sci. 2022 Jun 15:616:499-508. doi: 10.1016/j.jcis.2022.02.038. Epub 2022 Feb 12.

Authors

Wei Zhang¹, Chuan Jiang¹, Xin Guo², Mirza Muhammad Faran Ashraf Baig³, Caihong Ni¹, Shou-Jun Xiao⁴

Affiliations

¹ State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
² State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Current address : Bruker (Beijing) Scientific Technology Co. Ltd, China.
³ State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Current address : Laboratory of Biomedical Engineering and Biofunctional Materials, Faculty of Dentistry, The University of Hongkong, Hong Kong SAR, China.
⁴ State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China. Electronic address: sjxiao@nju.edu.cn.

PMID: 35228046
DOI: 10.1016/j.jcis.2022.02.038

Abstract

Hypothesis: Formation of coupled double crossovers (DXs) in a circular 106-mer oligonucleotide (c106nt) could generate stable tiles with the tile core span of 10 half turns. The large-span tiles with complicated curvatures and mechanics could assemble 2D lattices under different environments. Hence, 2D DNA lattice structures based on tile types and sequences, tile packing modes of corrugation and non-corrugation, and assembly media of solution and the substrate-solution interface are yet to be explored.

Experiments: Two c106nt scaffold strands with different sequences were synthesized. Four types of tiles, two rectilinear and two triangular tiles, were designed and their 2D assemblies were examined by atomic force microscopy (AFM).

Findings: The DX-coupled tiles provided fair strength and rigidity to assemble 2D lattices. Due to the complicated curvature and mechanics of tiles, the two-tile assemblies in solution displayed a few ripe lattices of ribbons, tubes, or polycrystalline aggregates as the minor products and tile oligomers as the major products; whereas the one-tile assemblies via substrate mediation exhibited well-organized monolayer lattices covering the whole mica disk. The herringbone packing patterns were first observed in DNA nanostructures. Based on the lattice constants and the surface coverages of lattices, we estimated the lattice yields for the substrate-mediated assemblies.

Keywords: Circular DNA; DNA nanotechnology; Solution assembly; Substrate-mediated assembly.

MeSH terms

DNA* / chemistry
Microscopy, Atomic Force
Nanostructures* / chemistry
Nanotechnology
Nucleic Acid Conformation
Oligonucleotides

Substances

Oligonucleotides
DNA