Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

Abstract

DNA tile-based assembly provides a promising bottom-up avenue to create designer two-dimensional (2D) and three-dimensional (3D) crystalline structures that may host guest molecules or nanoparticles to achieve novel functionalities. Herein, we introduce a new kind of DNA tiles (named layered-crossover tiles) that each consists of two or four pairs of layered crossovers to bridge DNA helices in two neighboring layers with precisely predetermined relative orientations. By providing proper matching rules for the sticky ends at the terminals, these layered-crossover tiles are able to assemble into 2D periodic lattices with precisely controlled angles ranging from 20° to 80°. The layered-crossover tile can be slightly modified and used to successfully assemble 3D lattice with dimensions of several hundred micrometers with tunable angles as well. These layered-crossover tiles significantly expand the toolbox of DNA nanotechnology to construct materials through bottom-up approaches.

Coarse-grained nucleic acid–protein model for hybrid nanotechnology

“…[17][18][19][20] Among the available tools, the oxDNA and oxRNA models [21][22][23][24] have been quite popular over the past few years, being used by dozens of research groups in over one hundred articles to study various aspects of DNA and RNA nanosystems including the biophysical properties of DNA and RNA. [25][26][27][28][29][30] Each nucleotide is represented as a rigid body in the simulation, with interactions between different sites parameterized to reproduce mechanical, structural and thermodynamic properties of single-stranded and double-stranded DNA and RNA respectively.…”

Constructing Large 2D Lattices Out of DNA-Tiles

“…In recent studies, Yan et al developed a derivative from the traditional double-crossover DNA motif, named layered-crossover tile to construct a set of rhombus-like layered-crossover DNA lattices. In the motif design, two or four-layered crossover tiles bridge neighboring layers with predetermined orientation [97]. Similarly, Qian and coworkers created a triangular tile that could form large 2D arrays and 3D shapes approximating a rhombic triacontahedron [101].…”

“…The lattice was self-assembled within a buffer with Ca 2+ /Na + ions during 90 min incubation [40]. (f) Design of layered-crossover tile and a corresponding image of a self-assembled 2D crystal structure [97]. Adapted with permission from [115] copyright 2019, [116] copyright 2016, [97] copyright 2018 American Chemical Society.…”

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation

“…To remedy this, several coarsegrained models have been developed [28][29][30][31][32][33][34][35][36] , each of which with a unique focus on a specific part of the DNA nanostructural design and characterization pipeline. In particular, the oxDNA/oxRNA models have grown in popularity in recent years and have been used for studying DNA/RNA nanostructures and devices 23,32,[37][38][39] as well as RNA/DNA biophysics 30,40,41 . The models represent each nucleotide as a single rigid body, where the interactions between nucleotides are empirically parameterized to reproduce basic structural, mechanical and thermodynamic properties of DNA and RNA FIG.…”