Automated sequence design of 2D wireframe DNA origami with honeycomb edges

Hyungmin Jun,William P Bricker,Mark Bathe,Xiao Wang

doi:10.1038/s41467-019-13457-y

Hyungmin Jun, William P Bricker + Show 2 more

Open Access

https://doi.org/10.1038/s41467-019-13457-y

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Journal: Nature Communications	Publication Date: Nov 28, 2019
Citations: 71	License type: open-access

Affiliation: Massachusetts Institute of Technology

Abstract

Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

Highlights

Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale
The designed edges for both PERDIX and METIS do not need to correspond to a multiple of a full turn of double helical B-form DNA (10.5-bp)[26,27], allowing for a significantly broader design space compared with other approaches that require discrete edge lengths based on the helicity of B-form DNA24
We introduce a DNA origami wireframe design procedure that combines the structural fidelity of bricklike designs with the geometric versatility of wireframe designs, encoded in the fully automatic, top-down design procedure METIS

Summary

Introduction

Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. 2D3 and 3D4,5 bricklike origami objects were designed using parallel duplexes assembled on square and honeycomb lattices largely to endow structural rigidity in 3D, and ease of manual scaffold routing in 2D and 3D, aided by the graphical design program caDNAno[6] that performs staple assignment semiautomatically Such 2D and 3D assemblies have been used for a variety of applications[1,2,7,8,9] including templating materials such as carbon nanotubes[10], metal nanowires[11], nanoparticle coordination[12,13,14,15], graphene sheets[16], and cell ligand patterning[2,17]. As in PERDIX26, unpaired scaffold nucleotides are introduced at vertices to accommodate 5′- and 3′end misalignments that allow for arbitrary edge lengths and vertex angles to be designed, facilitating the top-down specification of nearly arbitrary 2D shapes and topologies for nanoscale materials science and engineering

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